WO2013086354A1 - Biodegradable lipids for the delivery of active agents - Google Patents

Biodegradable lipids for the delivery of active agents Download PDF

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Publication number
WO2013086354A1
WO2013086354A1 PCT/US2012/068491 US2012068491W WO2013086354A1 WO 2013086354 A1 WO2013086354 A1 WO 2013086354A1 US 2012068491 W US2012068491 W US 2012068491W WO 2013086354 A1 WO2013086354 A1 WO 2013086354A1
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WIPO (PCT)
Prior art keywords
compound
lipid
alkyl
group
independently
Prior art date
Application number
PCT/US2012/068491
Other languages
French (fr)
Inventor
Martin Maier
Muthusamy Jayaraman
Akin Akinc
Shigeo Matsuda
Pachamuthu KADASAMY
Kallanthottathil G. Rajeev
Muthiah Manoharan
Original Assignee
Alnylam Pharmaceuticals, Inc.
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Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=47470195&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2013086354(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by Alnylam Pharmaceuticals, Inc. filed Critical Alnylam Pharmaceuticals, Inc.
Priority to CA2856742A priority Critical patent/CA2856742A1/en
Priority to EP21212055.4A priority patent/EP3988537A1/en
Priority to AU2012347637A priority patent/AU2012347637B2/en
Priority to EP12809020.6A priority patent/EP2788006A1/en
Priority to JP2014546124A priority patent/JP6305344B2/en
Publication of WO2013086354A1 publication Critical patent/WO2013086354A1/en
Priority to HK15100489.1A priority patent/HK1200089A1/en
Priority to AU2017276242A priority patent/AU2017276242A1/en

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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/16—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite containing nitrogen, e.g. nitro-, nitroso-, azo-compounds, nitriles, cyanates
    • A61K47/18—Amines; Amides; Ureas; Quaternary ammonium compounds; Amino acids; Oligopeptides having up to five amino acids
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    • A61K9/1272—Non-conventional liposomes, e.g. PEGylated liposomes, liposomes coated with polymers with substantial amounts of non-phosphatidyl, i.e. non-acylglycerophosphate, surfactants as bilayer-forming substances, e.g. cationic lipids
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    • C07C235/06—Carboxylic acid amides, the carbon skeleton of the acid part being further substituted by oxygen atoms having carbon atoms of carboxamide groups bound to acyclic carbon atoms and singly-bound oxygen atoms bound to the same carbon skeleton the carbon skeleton being acyclic and saturated having the nitrogen atoms of the carboxamide groups bound to hydrogen atoms or to acyclic carbon atoms
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    • C07C251/38—Oximes with oxygen atoms of oxyimino groups bound to hydrogen atoms or to carbon atoms of unsubstituted hydrocarbon radicals with the carbon atoms of the oxyimino groups bound to hydrogen atoms or to acyclic carbon atoms to carbon atoms of a saturated carbon skeleton
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    • C07C323/11—Thiols, sulfides, hydropolysulfides or polysulfides substituted by halogen, oxygen or nitrogen atoms, or by sulfur atoms not being part of thio groups containing thio groups and singly-bound oxygen atoms bound to the same carbon skeleton having the sulfur atoms of the thio groups bound to acyclic carbon atoms of the carbon skeleton
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Definitions

  • the present invention relates to biodegradable lipids and to their use for the delivery of active agents such as nucleic acids.
  • Therapeutic nucleic acids include, e.g., small interfering RNA (siRNA), micro RNA (miRNA), antisense oligonucleotides, ribozymes, plasmids, immune stimulating nucleic acids, antisense, antagomir, antimir, microRNA mimic, supermir, Ul adaptor, and aptamer.
  • siRNA or miRNA these nucleic acids can down-regulate intracellular levels of specific proteins through a process termed RNA interference (RNAi).
  • RNAi RNA interference
  • the therapeutic applications of RNAi are extremely broad, since siRNA and miRNA constructs can be synthesized with any nucleotide sequence directed against a target protein. To date, siRNA constructs have shown the ability to specifically down-regulate target proteins in both in vitro and in vivo models. In addition, siRNA constructs are currently being evaluated in clinical studies.
  • siRNA or miRNA constructs Two problems currently faced by siRNA or miRNA constructs are, first, their susceptibility to nuclease digestion in plasma and, second, their limited ability to gain access to the intracellular compartment where they can bind the protein RISC when administered systemically as the free siRNA or miRNA.
  • Lipid nanoparticles formed from cationic lipids with other lipid components, such as cholesterol and PEG lipids, and oligonucleotides (such as siRNA and miRNA) have been used to facilitate the cellular uptake of the oligonucleotides.
  • oligonucleotides such as siRNA and miRNA
  • these lipid nanoparticles would provide high drug:lipid ratios, protect the nucleic acid from degradation and clearance in serum, be suitable for systemic delivery, and provide intracellular delivery of the nucleic acid.
  • these lipid-nucleic acid particles should be well-tolerated and provide an adequate therapeutic index, such that patient treatment at an effective dose of the nucleic acid is not associated with significant toxicity and/or risk to the patient.
  • the present invention relates to a cationic lipid and PEG lipid suitable for forming nucleic acid-lipid particles.
  • Each of the cationic and PEG lipids of the present invention includes one or more biodegradable groups.
  • the biodegradable groups are located in a lipidic moiety (e.g., a hydrophobic chain) of the cationic or PEG lipid.
  • These cationic and PEG lipids may be incorporated into a lipid particle for delivering an active agent, such as a nucleic acid (e.g., an siRNA).
  • an active agent such as a nucleic acid (e.g., an siRNA).
  • the incorporation of the biodegradable group(s) into the lipid results in faster metabolism and removal of the lipid from the body following delivery of the active agent to a target area. As a result, these lipids have lower toxicity than similar lipids without the biodegradable groups.
  • the cationic lipid is a compound of formula (I), which has a branched alkyl at the alpha position adjacent to the biodegradable group (between the biodegradable group and the teriary carbon):
  • Formula (I) or a salt thereof e.g., a pharmaceutically acceptable salt thereof, wherein R' is absent, hydrogen, or alkyl (e.g., C C 4 alkyl); with respect to R 1 and R 2 ,
  • R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R 10 ;
  • R 1 and R 2 together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring;
  • one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl (e.g., a 6-member ring) with (a) the adjacent nitrogen atom and (b) the (R) a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR 3 R 4 )-; each occurrence of R 3 and R 4 are, independently H, halogen, OH, alkyl, alkoxy, -NH 2 , R 10 , alkylamino, or dialkylamino (in one preferred embodiment, each occurrence of R 3 and R 4 are, independently H or CrC 4 alkyl); each occurrence of R 10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(
  • X and Y are each, independently, alkylene or alkenylene (e.g., C 4 to C 2 o alkylene or C 4 to C 2 o alkenylene);
  • a biodegradable group e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)
  • each occurrence of R z is, independently, Q-Cg alkyl (e.g., methyl, ethyl, isopropyl, n- butyl, n-pentyl, or n-hexyl); a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3; and
  • Z and Z are each, independently, Cg-C 14 alkyl or Cg-C 14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a 1 2 double bond which is between the double bond and the terminus of Z or Z (e.g.,
  • the R'R R N-(R) a -Q-(R) b - group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment,
  • R and R are both alkyl (e.g., methyl).
  • a is 3. In another embodiment, b is 0.
  • a is 3, b is 0 and R is -CH 2 -. In yet a further embodiment, a is 3,
  • R is -CH 2 - and Q is -C(0)0-.
  • R and R are methyl, a is 3, b is 0, R is -CH 2 - and Q is -C(0)0-.
  • X and Y are each, independently -(CH 2 ) n - wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 )6-. In another embodiment, X and Y are -(CH 2 ) 7 -. In yet another embodiment, X and Y are -(CH 2 ) 9 -. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • M and M are each, independently, -OC(O)- or -C(0)0-.
  • M and M are each -C(0)0-.
  • the cationic lipid is a compound of formula (II), which has a branched alkyl at the alpha position adjacent to the biodegradable group (between the
  • Formula (II) or a salt thereof e.g., a pharmaceutically acceptable salt thereof, wherein R' is absent, hydrogen, or alkyl (e.g., C C 4 alkyl); with respect to R 1 and R 2 ,
  • R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R 10 ;
  • R 1 and R 2 together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring;
  • one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl (e.g., a 6-member ring) with (a) the adjacent nitrogen atom and (b) the (R) a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR 3 R 4 )-; each occurrence of R 3 and R 4 are, independently H, halogen, OH, alkyl, alkoxy, -NH 2 , R 10 , alkylamino, or dialkylamino (in one preferred embodiment, each occurrence of R 3 and R 4 are, independently H or CrC 4 alkyl); each occurrence of R 10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(
  • X and Y are each, independently, alkylene (e.g., C6-Cg alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
  • each occurrence of R z is, independently, Ci-Cg alkyl (e.g., methyl, ethyl, isopropyl); a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3; and
  • Z 1 and Z 2 are each, independently, C8-C 14 alkyl or C8-C 14 alkenyl, wherein (i) the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
  • M 1 or M 2 by at least 8 carbon atoms.
  • X and Y are each, independently -(CH 2 ) n - wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 ) 6 -. In another embodiment, X and Y are -(CH 2 ) -. In yet another embodiment, X and Y are -(CH 2 ) 9 -. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • R'R R N-(R) a -Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • the cationic lipid is a compound of formula (III), which has a branching point at a position that is 2-6 carbon atoms (i.e., at the beta ( ⁇ ), gamma ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ) or zeta position ⁇ )) adjacent to the biodegradable group (between the biodegradable group and the terminus of the tail, i.e., Z 1 or Z 2 ):
  • R', R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , M 1 , M 2 , R z , a, and b are defined as in formula (I);
  • L 1 and 1 2 are each, independently, C Cs alkylene or C2-C5 alkenylene;
  • X and Y are each, independently, alkylene (e.g., C 4 to C 2 o alkylene or C6-Cg alkylene) or alkenylene (e.g., C 4 to C 2 o alkenylene); and
  • Z 1 and Z 2 are each, independently, C 8 -C 14 alkyl or C 8 -C 14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
  • L 1 and L2 are each -CH 2 -. In another embodiment, L 1 and L2 are each -(CH 2 ) 2 -. In one embodiment, L 1 and L2 are each -(CH 1
  • X and Y are each, independently -(CH 2 ) n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 ) -. In another exemplary embodiment, X and Y are -(CH 2 ) 8 -. In yet another exemplary embodiment, X and Y are -(CH 2 )cr.
  • R'R R N-(R) a -Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • the cationic lipid is a compound of formula (IIIA), which has a branching point at a position that is 2-6 carbon atoms (i.e., at the beta ( ⁇ ), gamma ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ) or zeta position ⁇ )) from the biodegradable groups M 1 and M 2 (i.e., between the biodegradable group and the terminus of the tail, i.e., Z 1 or Z 2 ):
  • R', R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , M 1 , M 2 , a, and b are defined as in formula (I); each R z is, independently, Q-Cg alkyl (e.g., C 3 -C 6 alkyl or C 2 -C 3 alkyl);
  • L 1 and V 2 are each, independently, Q-Cs alkylene (e.g., C 2 -C 3 alkylene) or C 2 -C 5 alkenylene;
  • X and Y are each, independently, alkylene (e.g., C 4 to C 20 alkylene or C 7 -C 9 alkylene) or alkenylene (e.g., C 4 to C 20 alkenylene or C 7 -C 9 alkenylene); and
  • Z 1 and Z 2 are each, independently, Q-Cg alkyl (e.g., Ci-C 6 alkyl, such as Q, C 3 or C 5 alkyl) or C 2 -Cg alkenyl (such as C 2 -C 6 alkenyl); wherein said cationic lipid is not one selected from:
  • Q-Cg alkyl e.g., Ci-C 6 alkyl, such as Q, C 3 or C 5 alkyl
  • C 2 -Cg alkenyl such as C 2 -C 6 alkenyl
  • L 1 and L2 are each -(CH 2 ) 2 -. In another embodiment, L 1 and L2 are each -(CH 2 ) 3 -.
  • X and Y are each, independently -(CH 2 ) n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, 4 to 12 or 7-9. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10.
  • X and Y are -(CH 2 ) 7 -. In yet another exemplary embodiment, X and Y are -(CH 2 )9.
  • M 1 and M2 are -C(0)0- (where the carbonyl group in M 1 and M 2 is bound to the variable X, and the oxygen atom in M 1 and M2 is bound to the variable L 1 and L 2 ).
  • R'R R N-(R) a -Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • Z 1 and Z 2 are branched alkyl or branched alkenyl groups.
  • Z 1 , Z 2 , and each R z are C 3 -C8 alkyl (such as a C 3 - C 6 alkyl).
  • Z 1 , Z 2 , and each R z are C 3 -Cg branched alkyl (such as a C 3 -C 6 branched alkyl).
  • Z 1 , Z 2 , and each R z are C 3 -C8 straight alkyl (such as a C 3 -C 6 straight alkyl).
  • the branching point is at the second position (the ⁇ - position) from the biodegradable groups M 1 and M 2 in each tail.
  • Z 1 , Z 2 , and each R z can be C 3 - Cg alkyl (e.g., a C 3 -C 6 alkyl), such as a C 3 -Cg branched alkyl (e.g., a C 3 -C 6 branched alkyl) or a
  • C traight alkyl e.g., a C 3 -C 6 straight alkyl.
  • M 1 and M 2 3-C8 s are -
  • the branching point is at the third position (the ⁇ - position) from the biodegradable groups M 1 and M 2 in each tail.
  • Z 1 , Z 2 , and each R z can be C 3 - C8 alkyl (e.g., a C 3 -C 6 alkyl), such as a C 3 -C8 branched alkyl (e.g., a C 3 -C 6 branched alkyl) or a
  • C 3 -Cg straight alkyl e.g., a C 3 -C 6 straight alkyl.
  • M 1 and M 2 are -
  • the branching point is at the third position (the ⁇ - position) from the biodegradable groups M 1 and M 2 in each tail.
  • M 1 and/or M 2 are not -0(C(0)- (where the oxygen atom in M 1 and/or M2 is bound to the variable X, and the carbonyl in M 1 and/or M2 is bound to the variable L 1 and/or L 2 ).
  • Z 1 , Z 2 , and R z are not C3-Q0 cyclo alkyl (Ci-C6 alkyl).
  • the cationic lipid is a compound of formula (IV), which has a branching point at a position that is 2-6 carbon atoms (i.e., at beta ( ⁇ ), gamma ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ) or zeta position ⁇ )) adjacent to the biodegradable group (between the biodegradable group and the terminus of the tail i.e., Z 1 or Z 2 ):
  • R', R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , M 1 , M 2 , R z , a, and b are defined as in formula (I);
  • L 1 and L 2 are each, independently, C Cs alkylene or C2-C5 alkenylene;
  • X and Y are each, independently, alkylene or alkenylene (e.g., C 12 -C2o alkylene or C 12 - C 2 o alkenylene); and
  • each occurrence of Z is independently Q-C4 alkyl (preferably, methyl).
  • -L 1 -C(Z) 3 is -CH 2 C(CH 3 ) 3 .
  • - ⁇ ) 3 is -CH 2 CH 2 C(CH 3 ) 3 .
  • the total carbon atom content of each tail e.g., -X-M 1 -L 1 -C(Z) or -
  • Y-M 2 -L 2 -C(Z) ) is from about 17 to about 26.
  • the total carbon atom content can be from about 19 to about 26 or from about 21 to about 26.
  • X and Y are each, independently -(CH 2 ) n - wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 ) 6 -. In another embodiment, X and Y are -(CH 2 ) -. In yet another embodiment, X and Y are -(CH 2 ) 9 -. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • the cationic lipid is a compound of formula (V), which has an alkoxy or thioalkoxy (i.e., -S-alkyl) group substitution on at least one tail:
  • R', R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , M 1 , M 2 , a, and b are defined as in formula (I);
  • X and Y are each, independently, alkylene (e.g., C 6 -C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
  • Z 1 and Z 2 are each, independently, Cg-C 14 alkyl or Cg-C 14 alkenyl, wherein (i) the Cg-C 14 alkyl or Cs-C 14 alkenyl of at least one of Z 1 and Z 2 is substituted by one or more alkoxy (e.g., a CrC 4 alkoxy such as -OCH 3 ) or thioalkoxy (e.g., a CrC 4 thioalkoxy such as -SCH 3 ) groups, and (ii) the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2
  • alkoxy e.g., a CrC 4 alkoxy such as -OCH 3
  • thioalkoxy e.g., a CrC 4 thioalkoxy such as -SCH 3
  • the alkoxy substitution on Z 1 and/or Z 2 is at the beta position from the M 1 and/or M 2 group.
  • X and Y are each, independently -(CH 2 ) n - wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10.
  • X and Y are -(CH 2 ) 6 -. In another embodiment, X and Y are -(CH 2 ) 7 -. In yet another embodiment, X and Y are -(CH 2 )9-. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • R'R R N-(R) a -Q-(R)t > - group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • the cationic lipid is a compound of formula (VIA), which has one or more fluoro substituents on at least one tail at a position that is either alpha to a double bond or alpha to a biodegradable group:
  • R 1 , R 2 , R, a, and b are as defined with respect to formula (I);
  • R' is absent, hydrogen, or alkyl (e.g., C C 4 alkyl); and each of R 9 and R 10 are independently C 12 -C 24 alkyl (e.g., C 12 -C 2 o alkyl), C 12 -C 24 alkenyl (e.g., C 12 -C 2 o alkenyl), or C 12 -C 24 alkoxy (e.g., C 12 -C 20 alkoxy) (a) having one or more biodegradable groups and (b) optionally substituted with one or more fluorine atoms at a position which is (i) alpha to a biodegradable group and between the biodegradable group and the tertiary carbon atom marked with an asterisk (*), or (ii) alpha to a carbon-carbon double bond and between the double bond and the terminus of the R 9 or R 10 group; each biodegradable group independently interrupts the C 12 -C24 alkyl, alkenyl, or alkoxy
  • R 9 and R 10 contains a fluoro group
  • the terminus of R 9 and R 10 is separated from the tertiary carbon atom marked with an asterisk (*) by a chain of 18-22 carbon atoms (e.g., 18-20 carbon atoms).
  • the terminus of the R 9 and/or R 10 has the formula -C(0)0-CF 3 .
  • the cationic lipid is a compound of formula (VIB), which has one or more fluoro substituents on at least one tail at a position that is either alpha to a double bond or alpha to a biodegradable group:
  • R' , R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , M 1 , M 2 , a, and b are defined as in formula (I);
  • X and Y are each, independently, alkylene (e.g., C 6 -C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
  • Z and Z are each independently, Cg-C 14 alkyl or Cg-C 14 alkenyl, wherein said Cg-C 14 alkenyl is optionally substituted by one or more fluorine atoms at a position that is alpha to a
  • At least one of Z and Z is substituted by two fluoro groups at a position that is either alpha to a double bond or alpha to a biodegradable group.
  • At least one of Z and Z has a terminal -CF 3 group at a position that is alpha to a
  • biodegradable group i.e., at least one of Z and Z terminates with an -C(0)OCF 3 group.
  • At least one of Z and Z may include one or more of the following moieties:
  • X and Y are each, independently -(CH 2 ) n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 ) -. In another exemplary embodiment, X and Y are -(CH 2 ) 9 -. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • R'R R N-(R) a -Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • the cationic lipid is a compound of formula (VII), which has an acetal group as a biodegradable group in at least one tail:
  • R', R 1 , R 2 , R, R 3 , R 4 , R 10 , Q, R 5 , a, and b are defined as in formula (I);
  • X and Y are each, independently, alkylene (e.g., C 6 -C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
  • a biodegradable group e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C
  • Cio alkyl or C 4 -C 10 alkenyl) 1
  • Z 1 and Z 2 are each, independently, C 4 -C 14 alkyl or C 4 -C 14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
  • each of M 1 and M 2 is a same shape.
  • X and Y are each, independently -(CH 2 ) n - wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH 2 ) 6 -. In another embodiment, X and Y are -(CH 2 ) 7 -. In yet another embodiment, X and Y are -(CH 2 ) 9 -. In yet another embodiment, X and Y are -(CH 2 ) 8 -.
  • R'R R N-(R) a -Q-(R)t > - group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof.
  • the present invention relates to a cationic lipid or a salt thereof having:
  • each hydrophobic tail is of the formula -R e -M-R f where R e is a C 4 -C 14 alkyl or alkenyl, M is a biodegradable group, and R is a branched alkyl or alkenyl (e.g., a Cio-C2o alkyl or Cio-C2o alkenyl), such that (i) the chain length of -R e -M-R f is at most 20 atoms (i.e.
  • the total length of the tail from the first carbon atom after the central carbon atom to a terminus of the tail is at most 20), and (ii) the group -R e -M-R f has at least 20 carbon atoms (e.g., at least 21 atoms).
  • the alkyl or alkenyl group in R e may be substituted ith one or two fluorine atoms at
  • the alpha position to the M or M 2 group e.g., Also, optionally, the alkenyl group in R may be substituted with one or two fluorine atoms at the alpha position to a double
  • the cationic lipid of the present invention (such as of formulas I- VII) has assymetrical hydrophobic groups (i.e., the two hydrophobic groups have different chemical formulas).
  • the cationic lipid can have the formula: 3
  • G is branched or unbranched C3-C 15 alkyl, alkenyl or alkynyl (e.g., a n-Cg alkyl n-Cg alkyl, or n-C 10 alkyl);
  • R is a branched or unbranched alkylene or alkenylene (e.g., C 6 -C 20 alkylene or C 6 -C 20 alkenylene such as C 12 -C 2 o alkylene or C 12 -C 2 o alkenylene);
  • R 3 and R 4 are defined as in formula (I); each occurrence of R 5 is, independently, H or alkyl (e.g., C 1 -C4 alkyl);
  • R is branched or unbranched C3-C 15 alkyl, alkenyl or alkynyl;
  • a protonatable group having a pK a of from about 4 to about 13, more preferably from about 5 to about 8 (e.g. from about 5 to about 7, or from about 5 to about 6.5, or from about 5.5 to about 6.5, or from about 6 to about 6.5).
  • the primary group includes (i) a head group, and (ii) a central moiety (e.g., a central carbon atom) to which both the hydrophobic tails are directly bonded.
  • Representative central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group.
  • Representative asymmetrical cationic lipids include:
  • w is 0, 1, 2, or 3; and x and y are each independently 1, 2, 3, 4, 5, 6, or 7.
  • the biodegradable cationic lipid has a logP value of at least 10.1 (as calculated by the software available at http://www.molinspiration.com/services/logp.html from Molinspiration Cheminformatics of Slovensky Grob, Slovak Republic). More preferably, the logP value is at least 10.2 or 10.3.
  • the biodegradable cationic lipid in the lipid nanoparticle has a HPLC retention time (relative to the retention time of cholesterol in the lipid nanoparticle), hereafter referred to as tii pi( j - t c h ol , of at least 1.4.
  • HPLC retention time relative to the retention time of cholesterol in the lipid nanoparticle
  • biodegradable cationic lipid of the present invention is not one selected from:
  • the biodegradable cationic lipid is not one selected from those disclosed in International Publication No. WO 2011/153493 and U.S. Patent Publication No. 2012/0027803, both of which are hereby incorporated by reference.
  • biodegradable cationic lipid having (i) a logP value of at least 10.1 and/or a tii pi( j - t chol , of at least 1.4, and (2) one or more biodegradable groups (such as an ester group) located in the mid- or distal section of a lipidic moiety (e.g., a hydrophobic chain) of the cationic lipid, with the proviso that the compound is not selected from
  • the biodegradable cationic lipid is not one selected from those disclosed in International Publication No. WO 2011/153493 and U.S. Patent Publication No. 2012/0027803, both of which are hereby incorporated by reference.
  • the incorporation of the biodegradable group(s) into the cationic lipid results in faster metabolism and removal of the cationic lipid from the body following delivery of the active pharmaceutical ingredient to a target area.
  • the cationic lipid includes a branched alkyl or branched alkenyl group in its biodegradable group(s).
  • the cationic lipd has a logP of at least 10.2 or 10.3.
  • the cationic lipid has a tii pi( j - tchoh °f at least 1.75, 2.0, or 2.25.
  • the cationic lipid preferably has a pKa of from about 4 to about 7 (such as 6.0 to 6.5).
  • the cationic lipid having a logP value of at least 10.1 and/or a tu P id - tchoh °f at least 1.4 comprises (a) a head group (preferably a nitrogen containing head group, such as the head groups described herein), (b) at least two hydrophobic tails, each of the formula - (hydrophobic chain) -(biodegradable group)- (hydrophobic chain), and (c) a linker group (for instance, a single central carbon atom) which is bound to the head group and the hydrophobic tails.
  • the cationic lipid preferably has one, two, three, four or more of the properties listed below:
  • a pKa of from about 4 to about 7 (such as 6.0 to 6.5);
  • the biodegradable group is separated from the terminus of the hydrophobic tail by from about 6 to about 12 carbon atoms (for instance, 6 to 8 carbon atoms or 8 to 12 carbon atoms),
  • the chain length from the linker group to the terminus of the hydrophobic tail is at most 21 (e.g., at most 20, or from about 17 to about 21, from about 18 to about 20, or from about 16 to about 18) (The atom(s) in the linker group are not counted when calculating the chain length.);
  • the total number of carbon atoms in the hydrophobic tail is from about 17 to about 26 (such as from about 19 to about 26, or from about 21 to about 26);
  • the number of carbon atoms between the linker group and the biodegradable group ranges from about 5 to about 10 (for example, 6 to 10, or 7 to 9);
  • the total number of carbon atoms between the linker group and the terminus of the hydrophobic tail is from about 15 to about 20 (such as from 16 to 20, 16 to 18, or 18 to 20);
  • the total number of carbon atoms between the biodegradable group and the terminus of the hydrophobic tail is from about 12 to about 18 (such as from 13 to 25);
  • the terminal hydrophobic chain in the hydrophobic tail is a branched alkyl or alkenyl group, for example, where the branching occurs at the ⁇ , ⁇ , ⁇ , or ⁇ position on the hydrophobic chain relative to the biodegradable group;
  • the cationic lipid when formulated as a lipid nanoparticle (such as in Example 35), the cationic lipid has an in vivo half life (t 1/2 ) in the liver of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours;
  • the present invention embodies compounds having any combination of some or all of the aforementioned properties. These properties provide a cationic lipid which remains intact until delivery of an active agent, such as a nucleic acid, after which cleavage of the hydrophobic tail occurs in vivo.
  • the compounds can have all of properties (i) to (viii) (in addition to the logP or tii pi( j - t cll oi value).
  • the compounds have properties (i), (ii), (iii), and (viii).
  • the compounds have properties (i), (ii), (iii), (v), (vi), and (viii).
  • step (a) designing a cationic lipid having a logP value of at least 10.1 and/or a tii pi( j - t c h 0 i, of at least 1.4, and optionally also having one, two, three, four, or more properties from the list above (i.e., properties (i)-(xii)); and (b) synthesizing the cationic lipid of step (a).
  • the cationic lipid in step (a) may comprises (a) a head group (preferably a nitrogen containing head group, such as the head groups described herein), (b) at least two hydrophobic tails, each of the formula -(hydrophobic chain)- (biodegradable group)-(hydrophobic chain), and (c) a linker group (for instance, a single central carbon atom) which is bound to the head group and the hydrophobic tails.
  • Step (a) may comprise:
  • the PEG lipid has the formula:
  • Gi is branched or unbranched C 3 -C 15 alkyl, alkenyl or alkynyl (e.g., a n-C ⁇ alkyl n-C9 alkyl, or n-C 10 alkyl); or Gi is -R 12 -M R 13 ;
  • R is a branched or unbranched alkylene or alkenylene (e.g., C 6 -C 20 alkylene or C 6 -C 20 alkenylene such as C 12 -C 20 alkylene or Ci 2 -C 2 o alkenylene);
  • alkenylene e.g., C 6 -C 20 alkylene or C 6 -C 20 alkenylene such as C 12 -C 20 alkylene or Ci 2 -C 2 o alkenylene
  • R 3 and R 4 are defined as in formula (I); each occurrence of R 5 is, independently, H or alkyl (e.g., C 1 -C4 alkyl);
  • R is branched or unbranched C 3 -C 15 alkyl, alkenyl or alkynyl;
  • the pegylated primary group includes (i) a head group having a PEG moiety, and (ii) a central moiety (e.g., a central carbon atom) to which both the hydrophobic tails are directly bonded.
  • central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group.
  • 's include, but are not limited to,
  • b is 10-100 (e.g., 20-50 or 40-50)
  • PEG lipid (or a salt thereof) having: (i) a pegylated primary group including a head group which includes a PEG moiety (e.g., having from 10 to 1000 repeating units such as ethoxy units)), and
  • one or more hydrophobic tails (preferably, two hydrophobic tails) directly bound to the pegylated primary group, wherein at least one hydrophobic tail is of the formula -R e -M-R f where R e is a C 4 -C 14 alkyl or alkenyl, M is a biodegradable group, and R f is a branched alkyl or alkenyl (e.g., a Cio-C2o alkyl or Cio-C2o alkenyl), such that (i) the chain length of -R e -M-R f is at most 20 atoms (i.e.
  • the total length of the tail from the first carbon atom after the central carbon atom to a terminus of the tail is at most 20), and (ii) the group -R e -M-R f has at least 20 carbon atoms (e.g., at least 21 atoms).
  • the alkyl or alkenyl group in R e may be substituted
  • the alkenyl group in R may be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of R
  • the pegylated primary group includes (i) a head group having a PEG moiety, and (ii) a central moiety (e.g., a central carbon atom) to which the hydrophobic tails are directly bound.
  • the PEG moiety may have 5-100, 10-60, 15-50, or 20-45 repeating units.
  • the PEG moiety may have the formula u moiety wherein b is an integer from 10 to 1,000 (e.g., 5-100, 10-60, 15-50, or 20-45); R 3 is -H, -R c , or -OR c ; and R c is -H, alkyl (e.g., CrC 4 alkyl), acyl, cycloalkyl, alkenyl, alkynyl, aryl, heteroaryl, or heterocyclyl.
  • alkyl e.g., CrC 4 alkyl
  • acyl e.g., cycloalkyl
  • alkenyl alkynyl
  • aryl aryl
  • heteroaryl or heterocyclyl
  • lipid particle that includes a cationic lipid and/or PEG lipid of the present invention.
  • the lipid particle includes a cationic lipid of the present invention (e.g., of one of formulas (I)-(VIII)).
  • the lipid particle includes a PEG lipid of the present invention (e.g., of formula (IX)).
  • the lipid particle includes a cationic lipid of the present invention and a PEG lipid of the present invention.
  • the lipid particle includes a neutral lipid, a lipid capable of reducing aggregation, a cationic lipid, and optionally, a sterol (e.g., cholesterol).
  • Suitable neutral lipids include, but are not limited to, distearoylphosphatidylcholine (DSPC), dipalmitoylphosphatidylcholine (DPPC), POPC, DOPE, and SM.
  • Suitable lipids capable of reducing aggregation include, but are not limited to, a PEG lipid, such as PEG-DMA, PEG- DMG, and those of the present invention (e.g., of formula (IX)) or a combination thereof.
  • the lipid particle may further include an active agent (e.g., a therapeutic agent).
  • the active agent can be a nucleic acid such as a plasmid, an immuno stimulatory oligonucleotide, an siRNA, an antisense oligonucleotide, a microRNA, an antagomir, an aptamer, or a ribozyme.
  • the nucleic acid is a siRNA.
  • the nucleic acid is a miRNA.
  • the lipid particle includes a cationic lipid of the present invention, a neutral lipid and a sterol.
  • the lipid particle may further include an active agent, such as a nucleic acid (e.g., an siRNA or miRNA).
  • the lipid particle includes a PEG lipid of the present invention, a cationic lipid, a neutral lipid, and a sterol.
  • the lipid particle may further include an active agent, such as a nucleic acid (e.g., an siRNA or miRNA).
  • the lipid particles described herein may be lipid nanoparticles.
  • Yet another embodiment of the invention is a pharmaceutical composition which includes a lipid particle of the present invention and a pharmaceutically acceptable carrier.
  • the cationic lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
  • the PEG lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
  • the present invention relates to a method of delivering a nucleic acid molecule comprising administering a nucleic lipid particle comprising (i) the nucleic acid molecule and (ii) a cationic lipid and/or a PEG lipid of the present invention.
  • the cationic lipid and/or a PEG lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
  • the active agent can be a nucleic acid selected from a plasmid, an immuno stimulatory oligonucleotide, an siRNA, an antisense oligonucleotide, a microRNA, an antagomir, an aptamer, and a ribozyme.
  • the nucleic acid is a siRNA or miRNA.
  • Yet another aspect is a method of treating a disease or disorder characterized by the overexpression of a polypeptide in a subject by providing to the subject a pharmaceutical composition of the present invention, wherein the active agent is a nucleic acid selected from an siRNA, a microRNA, and an antisense oligonucleotide, and wherein the siRNA, microRNA, or antisense oligonucleotide includes a polynucleotide that specifically binds to a polynucleotide that encodes the polypeptide, or a complement thereof.
  • the nucleic acid is a siRNA or miRNA.
  • Yet another aspect is a method of treating a disease or disorder characterized by underexpression of a polypeptide in a subject by providing to the subject a pharmaceutical composition of the present invention, wherein the active agent is a plasmid that encodes the polypeptide or a functional variant or fragment thereof.
  • Yet another aspect is a method of inducing an immune response in a subject by providing to the subject a pharmaceutical composition wherein the active agent is an immuno stimulatory oligonucleotide.
  • composition or lipid particles described above include a nucleic acid.
  • the agent when contacted with cells, can efficiently deliver nucleic acids to the cells.
  • a method of delivering a nucleic acid to the interior of a cell by obtaining or forming a composition or lipid particles described above, and contacting the composition or lipid particles with a cell.
  • the present invention relates to a lipid particle that includes a neutral lipid, a lipid capable of reducing aggregation (e.g., a PEG lipid), a cationic lipid, and optionally a sterol.
  • the lipid particle further includes an active agent (e.g., a therapeutic agent).
  • an active agent e.g., a therapeutic agent.
  • the cationic lipid is a compound of any one of Formulas I- VIII.
  • the following disclosure represents various embodiments of the compounds described above, including the compounds of Formulas I- VIII.
  • M 1 and M 2 are each, independently:
  • M 1 and M 2 are each, independently:
  • M 1 and M 2 are each, independently:
  • M 1 and M 2 are each -C(0)0-.
  • R 1 and R 2 are each, individually, optionally substituted alkyl, cycloalkyl, cycloalkylalkyl, or heterocycle.
  • R 1 is alkyl and R 2 is alkyl, cycloalkyl or cycloalkylalkyl.
  • R 1 and R 2 are each, individually, alkyl (e.g.,
  • R 1 and R 2 are both methyl.
  • R 1 and R 2 together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring ( -methylpiperazinyl).
  • one of R 1 and R 2 is
  • R' is hydrogen or alkyl. In another embodiment, R' is hydrogen or methyl. In one embodiment, R' is absent. In one embodiment, R' is absent or methyl.
  • the compound also contains a negatively charged counter ion.
  • the counterion can be any anion, such as an organic or inorganic anion. Suitable examples of anions include, but are not limited to, tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, a-ketoglutarate, a-glycerophosphate, halide (e.g., chloride), sulfate, nitrate, bicarbonate, and carbonate.
  • the counterion is a halide (e.g., CI).
  • each R is, independently, -(CR 3 R 4 )-, wherein R 3 and R 4 are each, independently, H or alkyl (e.g., C C 4 alkyl).
  • each R is, independently, -(CHR 4 )-, wherein each R 4 is, independently H or alkyl (e.g., CrC 4 alkyl).
  • each R is, independently, -CH 2 -, -C(CH 3 ) 2 - or -CH(iPr)- (where iPr is isopropyl).
  • each R is -CH 2 -.
  • R 5 is, in each case, hydrogen or methyl.
  • R 5 can be, in each case, hydrogen.
  • Q is -C(0)0-.
  • the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R) a -Q- and the tertiary carbon adjacent to it (C*) form the following group:
  • n 1 to 4 (e.g., n is 2).
  • the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R) a -Q- and the tertiary carbon adjacent to it form the following group:
  • n 1 to 4 (e.g., n is 2)
  • R 1 , R 2 , R, a, and b are as defined with respect to formula (I).
  • a is 3.
  • the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R) a -Q- and the tertiary carbon adjacent to it form the following group:
  • n 1 to 4 (e.g., n is 2)
  • R 1 , R 2 , R, a, and b are as defined with respect to formula (I).
  • a is 0.
  • the group can be:
  • b is 0. In another embodiment, a is 2, 3, or 4 and b is 0. For example, in one embodiment, a is 3 and b is 0. In another embodiment, a is 3, b is 0, and Q is -C(0)0-.
  • a suitable cholesterol moiety for the cationic lipids of the present invention (including compounds of formulas I- VI) has the formula:
  • Additional embodiments include a cationic lipid having a head group, one or more hydrophobic tails, and a central moiety between the head group and the one or more tails.
  • the head group can include an amine; for example an amine having a desired pK a .
  • the pK a can be influenced by the structure of the lipid, particularly the nature of head group; e.g., the presence, absence, and location of functional groups such as anionic functional groups, hydrogen bond donor functional groups, hydrogen bond acceptor groups, hydrophobic groups (e.g., aliphatic groups), hydrophilic groups (e.g., hydroxyl or methoxy), or aryl groups.
  • the head group amine can be a cationic amine; a primary, secondary, or tertiary amine; the head group can include one amine group (monoamine), two amine groups (diamine), three amine groups (triamine), or a larger number of amine groups, as in an oligoamine or polyamine.
  • the head group can include a functional group that is less strongly basic than an amine, such as, for example, an imidazole, a pyridine, or a guanidinium group.
  • the head group can be zwitterionic. Other head groups are suitable as well.
  • central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group.
  • the central moiety can include, for example, a glyceride linker, an acyclic glyceride analog linker, or a cyclic linker (including a spiro linker, a bicyclic linker, and a polycyclic linker).
  • the central moiety can include functional groups such as an ether, an ester, a phosphate, a phosphonate, a phosphorothioate, a sulfonate, a disulfide, an acetal, a ketal, an imine, a hydrazone, or an oxime.
  • functional groups such as an ether, an ester, a phosphate, a phosphonate, a phosphorothioate, a sulfonate, a disulfide, an acetal, a ketal, an imine, a hydrazone, or an oxime.
  • Other central moieties and functional groups are suitable as well.
  • the cationic lipid is a racemic mixture.
  • the cationic lipid is enriched in one diastereomer, e.g. the cationic lipid has at least 95%, at least 90%, at least 80% or at least 70% diastereomeric excess.
  • the cationic lipid is enriched in one enantiomer, e.g. the lipid has at least 95%, at least 90%, at least 80% or at least 70% enantiomer excess.
  • the cationic lipid is chirally pure, e.g. is a single optical isomer.
  • the cationic lipid is enriched for one optical isomer.
  • a double bond e.g., a carbon-carbon double bond or carbon-nitrogen double bond
  • isomerism in the configuration about the double bond (i.e. cis/trans or E/Z isomerism).
  • the configuration of a double bond is illustrated in a chemical structure, it is understood that the corresponding isomer can also be present.
  • the amount of isomer present can vary, depending on the relative stabilities of the isomers and the energy required to convert between the isomers. Accordingly, some double bonds are, for practical purposes, present in only a single configuration, whereas others (e.g., where the relative stabilities are similar and the energy of conversion low) may be present as inseparable equilibrium mixture of configurations.
  • a double-bonded unsaturation is replaced by a cyclic unsaturation.
  • the cyclic unsaturation can be a cycloaliphatic unsaturation, e.g., a cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, or cyclooctyl group.
  • the cyclic group can be a polycyclic group, e.g., a bicyclic group or tricyclic group.
  • a bicyclic group can be bridged, fused, or have a spiro st oiety can be replaced by a cyclopropyl moiety, e.g.,
  • the cationic lipid includes one or more biodegradable groups.
  • the biodegradable group(s) include one or more bonds that may undergo bond breaking reactions in a biological environment, e.g., in an organism, organ, tissue, cell, or organelle.
  • Functional groups that contain a biodegradable bond include, for example, esters, dithiols, and oximes.
  • Biodegradation can be a factor that influences the clearance of the compound from the body when administered to a subject. Biodegredation can be measured in a cell based assay, where a formulation including a cationic lipid is exposed to cells, and samples are taken at various time points.
  • the lipid fractions can be extracted from the cells and separated and analyzed by LC-MS. From the LC-MS data, rates of biodegradation (e.g., as t values) can be measured.
  • Compound 1 includes an ester linkage in each aliphatic chain, which can undergo hydrolysis in a biological environment, for example, when exposed to, e.g., a lipase or an esterase.
  • the structure of the compound influences the rate at which the compound undergoes biodegradation.
  • a compound where the methyl substituent is on the other side of the biodegradable group such as would be expected to exhibit a different rate of biodegradation. Greater effects on that rate would be expected from changes in the structure of the compound at the site of hydrolysis.
  • One modification that can influence the rate of hydrolysis, and thereby influence the rate of biodegradation and clearance from a subject's body, is to make the leaving group of the hydrolysis reaction have a secondary, rather than primary, alcohol.
  • Compound 1 shown above may be metabolized as shown in the scheme below:
  • a cationic lipid of any of the embodiments described herein has an in vivo half life (t 1/2 ) (e.g., in the liver, spleen or plasma) of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours.
  • the cationic lipid preferably remains intact, or has a half-life sufficient to form a stable lipid nanoparticle which effectively delivers the desired active pharmaceutical ingredient (e.g., a nucleic acid) to its target but thereafter rapidly degrades to minimize any side effects to the subject.
  • the cationic lipid preferably has a ti /2 in the spleen of from about 1 to about 7 hours.
  • a cationic lipid of any of the embodiments described herein containing a biodegradable group or groups has an in vivo half life (t 1/2 ) (e.g., in the liver, spleen or plasma) of less than about 10% (e.g., less than about 7.5%, less than about 5%, less than about 2.5%) of that for the same cationic lipid without the biodegrable group or groups.
  • t 1/2 in vivo half life
  • Some cationic lipids can be conveniently represented as a hydrophobic group combined via a central moiety (such as a carbon atom) with a headgroup.
  • a central moiety such as a carbon atom
  • the present invention includes compounds composed of any combination of the head and hydrophobic groups listed below (in combination with a central moiety (such as a central carbon atom).
  • head groups include those depicted in Table 1A:
  • Suitable primary groups include, but are not limited to, those that are a combination of a head group from table 1A with a central carbon atom.
  • Other suitable primary groups include those in table IB below: Table IB
  • hydrophobic tail groups include those depicted in Table 1C:
  • tail groups includes those of the formula -R 12 -M 1 -R 13 where R 12 is a C 4 -
  • M 1 is a biodegradable group as defined above, and R 13 is a branched
  • alkyl or alkenyl e.g., a Cio-C 2 o alkyl or Q 0 -C 20 alkenyl
  • M 1 -R 13 is at most 21 atoms (i.e., the total length of the tail from the first carbon after the tertiary carbon (marked with an asterisk) to a terminus of the tail is at most 21), and (ii) the group -R 12 -
  • M 1 -R 13 has at least 20 carbon atoms (e.g., at least 21 or 22 carbon atoms).
  • the chain length of -R 12 -M 1 -R 13 is at most 21 (e.g., at most 20).
  • the chain length can be from about 17 to about 24 or from about 18 to about 20.
  • the total carbon atom content of each tail (-R 12 -M 1 -R 13 ) is from about 17 to about 26.
  • the total carbon atom content can be from about 19 to about 26 or from about 21 to about 26.
  • the tail has the formula: where R is an alkyl or alkenyl group having from about 13 to about 17 carbon atoms, and the total carbon length of the tail from the first carbon (the leftmost carbon atom above) to a terminus of the tail is at most 20.
  • the tail has from about 22 to about 26 carbon atoms.
  • the maximum length of R 13 from its attachment point to the ester group of the compound is 12 carbon atoms (e.g., the maximum length can be 11 carbon atoms).
  • the branch in the alkyl or alkenyl group is at the ⁇ -position or later from the point of attachment of R 13 to the ester group. Suitable R 13 groups include, but are not limited to
  • the cationic lipid can be any suitable cationic lipid.
  • the cationic lipid can be any suitable cationic lipid.
  • R is an alkyl or alkenyl group having from about 13 to about 15 carbon atoms
  • the total carbon length of the tail from the first carbon (i.e., the leftmost carbon atom, which is attached to a tertiary carbon) to a terminus of the tail is at most 20.
  • the tail has from about 24 to about 26 carbon atoms.
  • the maximum length of R 13 from its attachment point to the ester group of the compound is 10 carbon atoms (e.g., the maximum length can be 9 carbon atoms).
  • the branch in the alkyl or alkenyl group is at the ⁇ -position or later from the point of attachment of R 13 to the ester group. Suitable
  • R 13 groups include, but are not limited to
  • the cationic lipid can be any suitable cationic lipid.
  • the cationic lipid can be any suitable cationic lipid.
  • the R group may be derived from a natural product, such as dihydrocitgronellol, lavandulol, phytol, or dihydrophytol.
  • the R 13 group in the tails above is a dihydrocitronellol group (either as a racemic group or a chirally pure group):
  • the cationic lipid having a dihydroitronellol group can be any organic compound having a dihydroitronellol group.
  • the cationic lipid having a dihydroitronellol group can be any organic compound having a dihydroitronellol group.
  • the R group in the tails above is a lavandulol group or a homolog of it as shown below:
  • a cationic lipid of the fomula is a cationic lipid of the fomula:
  • Headgroup can also be thought of as a combination of a headgroup, a linker moiety, and two parts of the hydrophobic chains as follows:
  • headgrops Various headgrops, linker moieties, and hydrophobic chains I and II are listed below.
  • the present invention includes compounds composed of any combination of the head, linker, hydrophobic chain I, and hydrophobic chain II groups listed below.
  • cationic lipids of the present invention include those in Table 3 below. Each asymmetric carbon atom in the compounds below can be either chirally pure (R or S) or racemic. These cationic lipids as well as those in the working examples (such as Examples 36 and 37) are suitable for forming nucleic acid-lipid particles.
  • the present invention relates to a method of preparing a compound of Formula I-VII. Suitable exemplary synthetic methods are illustrated in Schemes 1-27 shown in the Examples section below.
  • the cationic lipid of the present invention is selected from the following compounds, and salts thereof (including pharmaceutically acceptable salts thereof). These cationic lipids are suitable for forming nucleic acid-lipid particles.
  • the cationic lipid of the present invention is selected from following compounds, and salts thereof (including pharmaceutically acceptable salts thereof):
  • the cationic lipid of the present invention is selected from the following compounds, and salts thereof (including pharmaceutically acceptable salts thereof):
  • Additional re resentative cationic lipids include, but are not limited to:
  • n 0, 1, or 2
  • X O, S, NR, CH 2
  • n 0, 1, or 2
  • n 0 1, or 2
  • n 0, 1, or 2
  • n 0 1, or 2
  • n 0, 1, or 2
  • the head can have one methylene unit between the X group (or other functional group) and nitrogen atom.
  • the head can be:
  • Cationic lipids include those having alternative fatty acid groups and other dialkylamino groups than those shown, including those in which the alkyl substituents are different (e.g., N-ethyl-N-methylamino-, and N-propyl-N-ethylamino-).
  • the cationic lipids have at least one protonatable or deprotonatable group, such that the lipid is positively charged at a pH at or below physiological pH (e.g. pH 7.4), and neutral at a second pH, preferably at or above physiological pH.
  • a pH at or below physiological pH e.g. pH 7.4
  • a second pH preferably at or above physiological pH.
  • Such lipids are also referred to as cationic lipids.
  • the lipids can have more than one protonatable or deprotonatable group, or can be zwiterrionic.
  • protonatable lipids i.e., cationic lipids
  • the lipids can have a pK a of about 4 to about 7, e.g., from about 5 to about 7, such as from about 5.5 to about 6.8, when incorporated into lipid particles.
  • Such lipids may be cationic at a lower pH formulation stage, while particles will be largely (though not completely) surface neutralized at physiological pH around pH 7.4.
  • the lipids are charged lipids.
  • charged lipid includes, but is not limited to, those lipids having one or two fatty acyl or fatty alkyl chains and a quaternary amino head group.
  • the quaternary amine carries a permanent positive charge.
  • the head group can optionally include an ionizable group, such as a primary, secondary, or tertiary amine that may be protonated at physiological pH.
  • the presence of the quaternary amine can alter the pKa of the ionizable group relative to the pKa of the group in a structurally similar compound that lacks the quaternary amine (e.g., the quaternary amine is replaced by a tertiary amine).
  • the cationic lipid can be a protonated salt of the amine cationic lipid.
  • the term "free form" refers to the amine cationic lipids in non-salt form.
  • the free form may be regenerated by treating the salt with a suitable dilute aqueous base solution such as dilute aqueous NaOH, potassium carbonate, ammonia and sodium bicarbonate.
  • the pharmaceutically acceptable salts of the instant cationic lipids can be synthesized from the cationic lipids of this invention which contain a basic or acidic moiety by conventional chemical methods.
  • the salts of the basic cationic lipids are prepared either by ion exchange chromatography or by reacting the free base with stoichiometric amounts or with an excess of the desired salt-forming inorganic or organic acid in a suitable solvent or various combinations of solvents.
  • the salts of the acidic compounds are formed by reactions with the appropriate inorganic or organic base.
  • non-toxic salts of the cationic lipids of this invention include non-toxic salts of the cationic lipids of this invention as formed by reacting a basic instant cationic lipids with an inorganic or organic acid.
  • non-toxic salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like, as well as salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, sulfanilic, 2-acetoxy-benzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, and trifluoroacetic (TFA
  • suitable “pharmaceutically acceptable salts” refers to salts prepared form pharmaceutically acceptable non-toxic bases including inorganic bases and organic bases.
  • Salts derived from inorganic bases include aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic salts, manganous, potassium, sodium, and zinc.
  • the base is selected from ammonium, calcium, magnesium, potassium and sodium.
  • Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as arginine, betaine caffeine, choline, N ⁇ -dibenzylethylenediamine, diethylamin, 2-diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylenediamine, N-ethylmorpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, isopropylamine, lysine, methylglucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethylamine, trimethylamine tripropylamine, and tromethamine.
  • basic ion exchange resins such as arginine, betaine caffeine,
  • the cationic lipids of the present invention may potentially be internal salts or zwitterions, since under physiological conditions a deprotonated acidic moiety in the compound, such as a carboxyl group, may be anionic, and this electronic charge might then be balanced off internally against the cationic charge of a protonated or alkylated basic moiety, such as a quaternary nitrogen atom.
  • a deprotonated acidic moiety in the compound such as a carboxyl group
  • a deprotonated acidic moiety in the compound such as a carboxyl group
  • this electronic charge might then be balanced off internally against the cationic charge of a protonated or alkylated basic moiety, such as a quaternary nitrogen atom.
  • One or more additional cationic lipids which carry a net positive charge at about physiological pH, in addition to those specifically described above, may also be included in the lipid particles and compositions described herein.
  • Such cationic lipids include, but are not
  • DOTMA N-(2,3-dioleyloxy)propyl-N,N-N-triethylammonium chloride
  • DDAB N,N-distearyl-N,N-dimethylammonium bromide
  • DOTAP N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride
  • DOTAP. CI N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride
  • DOTAP. CI l,2-Dioleyloxy-3-trimethylaminopropane chloride salt
  • DC-Choi N-(N',N'-dimethylaminoethane)-carbamoyl)cholesterol
  • DC-Choi N-(l-(2,3-dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate
  • DOSPA dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carboxyspermine
  • DOPE dioctadecylamidoglycyl carb
  • cationic lipids can be used, such as, e.g. , LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), and LIPOFECT AMINE (comprising DOSPA and DOPE, available from GIBCO/BRL).
  • LIPOFECTIN including DOTMA and DOPE, available from GIBCO/BRL
  • LIPOFECT AMINE comprising DOSPA and DOPE, available from GIBCO/BRL
  • Suitable head groups for the PEG lipids include, but are not limited to those shown in Table 3 below.
  • n is an integer from 10 to 100 (e.g. 20-50 or 40-50);
  • s, s', t and t' are independently 0, 1, 2, 3, 4, 5, 6 or 7; and m is 1, 2, 3, 4, 5, or 6.
  • the lipid particles and compositions described herein may also include one or more neutral lipids.
  • Neutral lipids when present, can be any of a number of lipid species which exist either in an uncharged or neutral zwitterionic form at physiological pH.
  • Such lipids include, for example, diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, dihydrosphingomyelin, cephalin, and cerebrosides.
  • the neutral lipid component is a lipid having two acyl groups (e.g., diacylphosphatidylcholine and diacylphosphatidylethanolamine).
  • the neutral lipid contains saturated fatty acids with carbon chain lengths in the range of C 10 to C 2 o- In another embodiment, the neutral lipid includes mono or diunsaturated fatty acids with carbon chain lengths in the range of C 10 to C 20 .
  • Suitable neutral lipids include, but are not limited to, DSPC, DPPC, POPC, DOPE, DSPC, and SM.
  • the lipid particles and compositions described herein may also include one or more lipids capable of reducing aggregation.
  • lipids that reduce aggregation of particles during formation include polyethylene glycol (PEG)-modified lipids (PEG lipids, such as PEG-DMG and PEG-DMA), monosialoganglioside Gml, and polyamide oligomers ("PAO”) such as (described in U.S. Patent No. 6,320,017, which is incorporated by reference in its entirety).
  • Suitable PEG lipids include, but are not limited to, PEG-modified phosphatidylethanolamine and phosphatidic acid, PEG-ceramide conjugates (e.g., PEG-CerC14 or PEG-CerC20) (such as those described in U.S. Patent No. 5,820,873, incorporated herein by reference), PEG-modified dialkylamines and PEG-modified l,2-diacyloxypropan-3-amines, PEG-modified diacylglycerols and dialkylglycerols, mPEG (mw2000)-diastearoylphosphatidylethanolamine (PEG-DSPE).
  • the lipid particles and compositions may include a sterol, such as cholesterol.
  • the present invent relates to lipid particles that include one or more of the cationic lipids described herein.
  • the lipid particle includes one or more compounds of formula I- VII.
  • Lipid particles include, but are not limited to, liposomes.
  • a liposome is a structure having lipid-containing membranes enclosing an aqueous interior.
  • nucleic acid- lipid particle comprising a cationic lipid of the present invention, a non-cationic lipid (such as a neutral lipid), optionally a PEG-lipid conjugate (such as the lipids for reducing aggregation of lipid particles discussed herein), optionally a sterol (e.g., cholesterol), and a nucleic acid.
  • SNALP refers to a stable nucleic acid-lipid particle.
  • a SNALP represents a particle made from lipids, wherein the nucleic acid (e.g., an interfering RNA) is encapsulated within the lipids.
  • SNALPs are useful for systemic applications, as they can exhibit extended circulation lifetimes following intravenous (i.v.) injection, they can accumulate at distal sites (e.g., sites physically separated from the administration site), and they can mediate silencing of target gene expression at these distal sites.
  • the nucleic acid may be complexed with a condensing agent and encapsulated within a SNALP as set forth in International Publication No. WO 00/03683, the disclosure of which is herein incorporated by reference in its entirety.
  • the lipid particle may include a cationic lipid, a fusion-promoting lipid (e.g., DPPC), a neutral lipid, cholesterol, and a PEG-modified lipid.
  • the lipid particle includes the above lipid mixture in molar ratios of about 20-70% cationic lipid: 0.1-50% fusion promoting lipid: 5-45% neutral lipid: 20-55% cholesterol: 0.5-15% PEG-modified lipid (based upon 100% total moles of lipid in the lipid particle).
  • the cationic lipid is present in a mole percentage of about 20% and about 60%; the neutral lipid is present in a mole percentage of about 5% to about 25%; the sterol is present in a mole percentage of about 25% to about 55%; and the PEG lipid is PEG-DMA, PEG-DMG, or a combination thereof, and is present in a mole percentage of about 0.5% to about 15% (based upon 100% total moles of lipid in the lipid particle).
  • the molar lipid ratio with regard to mol% cationic lipid/DSPC/Chol/PEG-DMG or PEG-DMA) is approximately 40/10/40/10, 35/15/40/10 or 52/13/30/5.
  • This mixture may be further combined with a fusion-promoting lipid in a molar ratio of 0.1-50%, 0.1-50%, 0.5-50%, 1-50%, 5%-45%, 10%-40%, or 15%-35%.
  • the resulting lipid particles can have a total molar ratio of (mol% cationic lipid/DSPC/Chol/PEG-DMG or PEG-DMA/fusion-promoting peptide) 20/5/20/5/50.
  • the neutral lipid, DSPC, in these compositions is replaced with POPC, DPPC, DOPE or SM.
  • the lipid particles comprise a cationic lipid of the present invention, a neutral lipid, a sterol and a PEG-modified lipid.
  • the lipid particles include from about 25% to about 75% on a molar basis of cationic lipid, e.g., from about 35 to about 65%, from about 45 to about 65%, about 60%, about 57.5%, about 57.1%, about 50% or about 40% on a molar basis.
  • the lipid particles include from about 0% to about 15% on a molar basis of the neutral lipid, e.g., from about 3 to about 12%, from about 5 to about 10%, about 15%, about 10%, about 7.5%, about 7.1% or about 0% on a molar basis.
  • the neutral lipid is DPPC.
  • the neutral lipid is DSPC.
  • the formulation includes from about 5% to about 50% on a molar basis of the sterol, e.g., about 15 to about 45%, about 20 to about 40%, about 48%, about 40%, about 38.5%, about 35%, about 34.4%, about 31.5% or about 31% on a molar basis.
  • the sterol is cholesterol.
  • the lipid particles described herein may further include one or more therapeutic agents.
  • the lipid particles include a nucleic acid (e.g., an oligonucleotide), such as siRNA or miRNA.
  • the lipid particles include from about 0.1% to about 20% on a molar basis of the PEG-modified lipid, e.g., about 0.5 to about 10%, about 0.5 to about 5%, about 10%, about 5%, about 3.5%, about 1.5%, about 0.5%, or about 0.3% on a molar basis.
  • the PEG-modified lipid is PEG- DMG.
  • the PEG-modified lipid is PEG-c-DMA.
  • the lipid particles include 25-75% of cationic lipid, 0.5-15% of the neutral lipid, 5-50% of the sterol, and 0.5- 20% of the PEG-modified lipid on a molar basis.
  • the lipid particles include 35-65% of cationic lipid, 3-12% of the neutral lipid, 15-45% of the sterol, and 0.5- 10% of the PEG-modified lipid on a molar basis. In one embodiment, the lipid particles include 45-65% of cationic lipid, 5-10% of the neutral lipid, 25-40% of the sterol, and 0.5- 5% of the PEG-modified lipid on a molar basis. In one embodiment, the PEG modified lipid comprises a PEG molecule of an average molecular weight of 2,000 Da. In one embodiment, the PEG modified lipid is PEG-distyryl glycerol (PEG-DSG).
  • PEG-DSG PEG-distyryl glycerol
  • the ratio of lipid: siRNA is at least about 0.5: 1, at least about 1: 1, at least about 2: 1, at least about 3: 1, at least about 4: 1, at least about 5: 1, at least about 6: 1, at least about 7: 1, at least about 11: 1 or at least about 33: 1. In one embodiment, the ratio of lipid: siRNA ratio is between about 1: 1 to about 35: 1, about 3: 1 to about 15: 1, about 4: 1 to about 15: 1, or about 5: 1 to about 13: 1. In one embodiment, the ratio of lipid: siRNA ratio is between about 0.5: 1 to about 12: 1.
  • the lipid particles are nanoparticles.
  • the lipid particles have a mean diameter size of from about 50 nm to about 300 nm, such as from about 50 nm to about 250 nm, for example, from about 50 nm to about 200 nm.
  • a lipid particle containing a cationic lipid of any of the embodiments described herein has an in vivo half life (t ⁇ ) (e.g., in the liver, spleen or plasma) of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours.
  • t ⁇ in vivo half life
  • a lipid particle containing a cationic lipid of any of the embodiments described herein has an in vivo half life (t ⁇ ) (e.g., in the liver, spleen or plasma) of less than about 10 % (e.g., less than about 7.5%, less than about 5%, less than about 2.5%) of that for the same cationic lipid without the biodegrable group or groups.
  • t ⁇ in vivo half life
  • the lipid particles and compositions described herein can further include one or more antioxidants.
  • the antioxidant stabilizes the lipid particle and prevents, decreases, and/or inhibits degradation of the cationic lipid and/or active agent present in the lipid particles.
  • the antioxidant can be a hydrophilic antioxidant, a lipophilic antioxidant, a metal chelator, a primary antioxidant, a secondary antioxidant, salts thereof, and mixtures thereof.
  • the antioxidant comprises a metal chelator such as EDTA or salts thereof, alone or in combination with one, two, three, four, five, six, seven, eight, or more additional antioxidants such as primary antioxidants, secondary antioxidants, or other metal chelators.
  • the antioxidant comprises a metal chelator such as EDTA or salts thereof in a mixture with one or more primary antioxidants and/or secondary antioxidants.
  • the antioxidant may comprise a mixture of EDTA or a salt thereof, a primary antioxidant such as a- tocopherol or a salt thereof, and a secondary antioxidant such as ascorbyl palmitate or a salt thereof.
  • the antioxidant comprises at least about 100 mM citrate or a salt thereof. Examples of antioxidants include, but are not limited to, hydrophilic antioxidants, lipophilic antioxidants, and mixtures thereof.
  • Non-limiting examples of hydrophilic antioxidants include chelating agents (e.g., metal chelators) such as ethylenediaminetetraacetic acid (EDTA), citrate, ethylene glycol tetraacetic acid (EGTA), l,2-bis(o-aminophenoxy)ethane-N,N,N',N'- tetraacetic acid (BAPTA), diethylene triamine pentaacetic acid (DTPA), 2,3-dimercapto-l- propanesulfonic acid (DMPS), dimercap to succinic acid (DMSA), cc-lipoic acid, salicylaldehyde isonicotinoyl hydrazone (SIH), hexyl thioethylamine hydrochloride (HTA), desferrioxamine, salts thereof, and mixtures thereof.
  • metal chelators e.g., metal chelators
  • EDTA ethylenediaminetetraacetic acid
  • Additional hydrophilic antioxidants include ascorbic acid, cysteine, glutathione, dihydrolipoic acid, 2- mercaptoethane sulfonic acid, 2- mercaptobenzimidazole sulfonic acid, 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid, sodium metabisulfite, salts thereof, and mixtures thereof.
  • Non-limiting examples of lipophilic antioxidants include vitamin E isomers such as ⁇ -, ⁇ -, ⁇ -, and ⁇ -tocopherols and ⁇ -, ⁇ -, ⁇ -, and ⁇ - tocotrienols; polyphenols such as 2-tert-butyl-4-methyl phenol, 2-fert-butyl-5-methyl phenol, and 2-tert-butyl-6-methyl phenol; butylated hydroxyanisole (BHA) (e.g., 2-teri-butyl-4- hydroxyanisole and 3-tert-butyl-4-hydroxyanisole); butylhydroxytoluene (BHT); tert- butylhydroquinone (TBHQ); ascorbyl palmitate; rc-propyl gallate; salts thereof; and mixtures thereof.
  • Suitable antioxidants and formulations containing such antioxidants are described in International Publication No. WO 2011/066651, which is hereby incorporated by reference.
  • the lipid particles or compositions contain the antioxidant EDTA (or a salt thereof), the antioxidant citrate (or a salt thereof), or EDTA (or a salt thereof) in combination with one or more (e.g., a mixture of) primary and/or secondary antioxidants such as a- tocopherol (or a salt thereof) and/or ascorbyl palmitate (or a salt thereof).
  • one or more e.g., a mixture of
  • primary and/or secondary antioxidants such as a- tocopherol (or a salt thereof) and/or ascorbyl palmitate (or a salt thereof).
  • the antioxidant is present in an amount sufficient to prevent, inhibit, or reduce the degradation of the cationic lipid present in the lipid particle.
  • the antioxidant may be present at a concentration of at least about or about 0.1 mM, 0.5 mM, 1 mM, 10 mM, 100 mM, 500 mM, 1 M, 2 M, or 5M, or from about 0.1 mM to about 1 M, from about 0.1 mM to about 500 mM, from about 0.1 mM to about 250 mM, or from about 0.1 mM to about 100 mM.
  • lipid particles and compositions described herein can further include an apolipoprotein.
  • apolipoprotein or “lipoprotein” refers to apolipoproteins known to those of skill in the art and variants and fragments thereof and to apolipoprotein agonists, analogues or fragments thereof described below.
  • the active agent is a nucleic acid, such as a siRNA.
  • the active agent can be a nucleic acid encoded with a product of interest, including but not limited to, RNA, antisense oligonucleotide, an antagomir, a DNA, a plasmid, a ribosomal RNA (rRNA), a micro RNA (miRNA) (e.g., a miRNA which is single stranded and 17-25 nucleotides in length), transfer RNA (tRNA), a small interfering RNA (siRNA), small nuclear RNA (snRNA), antigens, fragments thereof, proteins, peptides, vaccines and small molecules or mixtures thereof.
  • RNA antisense oligonucleotide
  • an antagomir e.g., a DNA, a plasmid, a ribosomal RNA (rRNA), a micro RNA (miRNA) (e.g., a mi
  • the nucleic acid is an oligonucleotide (e.g., 15-50 nucleotides in length (or 15-30 or 20-30 nucleotides in length)).
  • An siRNA can have, for instance, a duplex region that is 16-30 nucleotides long.
  • the nucleic acid is an immuno stimulatory oligonucleotide, decoy oligonucleotide, supermir, miRNA mimic, or miRNA inhibitor.
  • a supermir refers to a single stranded, double stranded or partially double stranded oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or both or modifications thereof, which has a nucleotide sequence that is substantially identical to an miRNA and that is antisense with respect to its target.
  • miRNA mimics represent a class of molecules that can be used to imitate the gene silencing ability of one or more miRNAs.
  • miRNA mimic refers to synthetic non-coding RNAs (i.e. the miRNA is not obtained by purification from a source of the endogenous miRNA) that are capable of entering the RNAi pathway and regulating gene expression.
  • the nucleic acid that is present in a lipid-nucleic acid particle can be in any form.
  • the nucleic acid can, for example, be single-stranded DNA or RNA, or double- stranded DNA or RNA, or DNA-RNA hybrids.
  • Non-limiting examples of double- stranded RNA include siRNA.
  • Single- stranded nucleic acids include, e.g. , antisense oligonucleotides, ribozymes, microRNA, and triplex-forming oligonucleotides.
  • the lipid particles of the present invention can also deliver nucleic acids which are conjugated to one or more ligands.
  • the lipid particles may be formulated as a pharmaceutical composition, e.g., which further comprises a pharmaceutically acceptable diluent, excipient, or carrier, such as physiological saline or phosphate buffer.
  • a pharmaceutically acceptable diluent, excipient, or carrier such as physiological saline or phosphate buffer.
  • the resulting pharmaceutical preparations may be sterilized by conventional, well known sterilization techniques.
  • the aqueous solutions can then be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, and tonicity adjusting agents, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, and calcium chloride.
  • the lipidic suspension may include lipid-protective agents which protect lipids against free -radical and lipid-peroxidative damages on storage. Lipophilic free-radical quenchers, such as a-tocopherol and water-soluble iron-specific chelators, such as ferrioxamine, are suitable.
  • the concentration of lipid particle or lipid-nucleic acid particle in the pharmaceutical formulations can vary, for example, from less than about 0.01%, to at or at least about 0.05-5% to as much as 10 to 30% by weight.
  • a solution of one or more lipids (including a cationic lipid of any of the embodiments described herein) in an organic solution (e.g., ethanol) is prepared.
  • a solution of one or more active (therapeutic) agents (such as, for example an siRNA molecule or a 1: 1 molar mixture of two siRNA molecules) in an aqueous buffered (e.g., citrate buffer) solution is prepared.
  • the two solutions are mixed and diluted to form a colloidal suspension of siRNA lipid particles.
  • the siRNA lipid particles have an average particle size of about 80-90 nm.
  • the dispersion may be filtered through 0.45/2 micron filters, concentrated and diafiltered by tangential flow filtration.
  • cationic lipid inlcudes those lipids having one or two fatty acid or fatty aliphatic chains and an amino acid containing head group that may be protonated to form a cationic lipid at physiological pH.
  • a cationic lipid is referred to as an "amino acid conjugate cationic lipid.”
  • a subject or patient in whom administration of the complex is an effective therapeutic regimen for a disease or disorder is preferably a human, but can be any animal, including a laboratory animal in the context of a clinical trial or screening or activity experiment.
  • the methods, compounds and compositions of the present invention are particularly suited to administration to any animal, particularly a mammal, and including, but by no means limited to, humans, domestic animals, such as feline or canine subjects, farm animals, such as but not limited to bovine, equine, caprine, ovine, and porcine subjects, wild animals (whether in the wild or in a zoological garden), research animals, such as mice, rats, rabbits, goats, sheep, pigs, dogs, and cats, avian species, such as chickens, turkeys, and songbirds, i.e., for veterinary medical use.
  • biodegradable cationic lipid refers to a cationic lipid having one or more biodegradable groups located in the mid- or distal section of a lipidic moiety (e.g., a hydrophobic chain) of the cationic lipid.
  • a lipidic moiety e.g., a hydrophobic chain
  • biodegradable group refers to a group that include one or more bonds that may undergo bond breaking reactions in a biological environment, e.g., in an organism, organ, tissue, cell, or organelle.
  • the biodegradable group may be metabolizable by the body of a mammal, such as a human (e.g., by hydrolysis).
  • Some groups that contain a biodegradable bond include, for example, but are not limited to esters, dithiols, and oximes.
  • an "aliphatic” group is a non-aromatic group in which carbon atoms are linked into chains, and is either saturated or unsaturated.
  • alkyl and alkylene refer to a straight or branched chain saturated hydrocarbon moiety.
  • the alkyl group is a straight chain saturated hydrocarbon.
  • the "alkyl” or “alkylene” group contains from 1 to 24 carbon atoms.
  • Representative saturated straight chain alkyl groups include methyl, ethyl, n-propyl, n-butyl, n-pentyl, and n-hexyl.
  • Representative saturated branched alkyl groups include isopropyl, sec-butyl, isobutyl, ie/t-butyl, and isopentyl.
  • alkenyl refers to a straight or branched chain hydrocarbon moiety having one or more carbon-carbon double bonds. In one embodiment, the alkenyl group contains 1, 2, or 3 double bonds and is otherwise saturated. Unless otherwise specified, the "alkenyl” group contains from 2 to 24 carbon atoms. Alkenyl groups include both cis and trans isomers. Representative straight chain and branched alkenyl groups include ethylenyl, propylenyl,
  • alkynyl refers to a straight or branched chain hydrocarbon moiety having one or more carbon-carbon triple bonds. Unless otherwise specified, the "alkynyl” group contains from 2 to 24 carbon atoms. Representative straight chain and branched alkynyl groups include acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, and 3-methyl-l-butynyl.
  • branched alkyl refers to an alkyl, alkenyl, or alkynyl group in which one carbon atom in the group (1) is bound to at least three other carbon atoms and (2) is not a ring atom of a cyclic group.
  • a spirocyclic group in an alkyl, alkenyl, or alkynyl group is not considered a point of branching.
  • acyl refers to a carbonyl group substituted with hydrogen, alkyl, partially saturated or fully saturated cycloalkyl, partially saturated or fully saturated heterocycle, aryl, or heteroaryl.
  • acyl groups include groups such as (C 1 -C2o)alkanoyl (e.g., formyl, acetyl, propionyl, butyryl, valeryl, caproyl, and t-butylacetyl), (C3-C2o)cycloalkylcarbonyl (e.g., cyclopropylcarbonyl, cyclobutylcarbonyl, cyclopentylcarbonyl, and cyclohexylcarbonyl), heterocyclic carbonyl (e.g., pyrrolidinylcarbonyl, pyrrolid-2-one-5-carbonyl, piperidinylcarbonyl, piperazinylcarbonyl, and tetrahydrofurany
  • aryl refers to an aromatic monocyclic, bicyclic, or tricyclic hydrocarbon ring system. Unless otherwise specified, the "aryl” group contains from 6 to 14 carbon atoms. Examples of aryl moieties include, but are not limited to, phenyl, naphthyl, anthracenyl, and pyrenyl.
  • cycloalkyl and cycloalkylene refer to a saturated monocyclic or bicyclic hydrocarbon moiety such as cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Unless otherwise specified, the "cycloalkyl” or “cycloalkylene” group contains from 3 to 10 carbon atoms.
  • cycloalkylalkyl refers to a cycloalkyl group bound to an alkyl group, where the alkyl group is bound to the rest of the molecule.
  • heterocycle refers to a non-aromatic 5- to 8-membered monocyclic, or 7- to 12-membered bicyclic, or 11- to 14-membered tricyclic ring system which is either saturated or unsaturated, and which contains from 1 to 3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, independently selected from nitrogen, oxygen and sulfur, and wherein the nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen heteroatom may be optionally quaternized.
  • the heterocycle may be a cycloalkoxy group.
  • heterocycle may be attached to the rest of the molecule via any heteroatom or carbon atom in the heterocycle.
  • Heterocycles include, but are not limited to, morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, piperizynyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydroprimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, and tetrahydrothiopyranyl.
  • heteroaryl refers to an aromatic 5-8 membered monocyclic, 7-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, where the heteroatoms are selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S if monocyclic, bicyclic, or tricyclic, respectively).
  • the heteroaryl groups herein described may also contain fused rings that share a common carbon-carbon bond.
  • substituted refers to the replacement of one or more hydrogen radicals in a given structure with the radical of a specified substituent including, but not limited to: halo, alkyl, alkenyl, alkynyl, aryl, heterocyclyl, thiol, alkylthio, oxo, thioxy, arylthio, alkylthioalkyl, arylthioalkyl, alkylsulfonyl, alkylsulfonylalkyl, arylsulfonylalkyl, alkoxy, aryloxy, aralkoxy, aminocarbonyl, alkylaminocarbonyl, arylaminocarbonyl, alkoxycarbonyl, aryloxycarbonyl, haloalkyl, amino, trifluoromethyl, cyano, nitro, alkylamino, arylamino, alkylaminoalkyl, arylamin
  • halogen refers to fluoro, chloro, bromo and iodo.
  • DSPC distearoylphosphatidylcholine
  • DPPC l,2-Dipalmitoyl-sn-glycero-3-phosphocholine
  • POPC 1- palmitoyl-2-oleoyl-sn-phosphatidylcholine
  • DOPE l,2-dileoyl-sn-3- phosphoethanolamine
  • PEG-DMG generally refers to 1,2-dimyristoyl-sn-glycerol-methoxy polyethylene glycol (e.g., PEG 2000)
  • TBDPSC1 tert-Butylchlorodiphenylsilane
  • DMAP DMAP:
  • HMPA hexamethylphosphoramide
  • EDC l-ethyl-3-(3- dimethylaminopropyl) carbodiimide
  • DIPEA diisopropylethylamine
  • DCM dichloromethane
  • TEA triethylamine
  • TBAF tetrabutylammonium fluoride
  • protecting groups are any group that reduces or eliminates unwanted reactivity of a functional group.
  • a protecting group can be added to a functional group to mask its reactivity during certain reactions and then removed to reveal the original functional group.
  • an “alcohol protecting group” is used.
  • An “alcohol protecting group” is any group which decreases or eliminates unwanted reactivity of an alcohol functional group.
  • the compounds may be prepared by at least one of the techniques described herein or known organic synthesis techniques.
  • the di-aldehyde 4 can be synthesized as shown in Scheme 3, using l-bromo-9-decene.
  • Di- aldehyde containing a head group 27 can be useful for the synthesis of terminal ester-substituted lipids using, e.g., a Wittig reaction. Ozonolysis can afford di-aldehyde 4 and 27.
  • Compound 30 Compound 29 (133 g, 0.5635 mol) was dissolved in 1.5 L of DCM, CBr 4 (280.35 g, 0.8456 mol) was added into this stirring solution and the reaction mixture was cooled to 0°C under an inert atmosphere. PPh 3 (251.03 g, 0.9571 mol) was then added in portions keeping the temperature below 20 °C. After complete addition, the reaction mixture was stirred for 3 hours at room temperature. After completion of the reaction, the solid (PPh 3 0) that precipitated from the reaction mixture was removed by filtration, and the filtrate was diluted with crushed ice ( ⁇ 1.5 kg) and extracted with DCM (3 x 750 mL).
  • the organic layer was taken in 5 litre beaker, diluted with 500 mL of methanol and cooled to 0 °C. To this solution, an excess of NaBH 4 ( ⁇ 5eq) was added in portions to ensure hydrolysis of the formate ester which was not cleaved by addition of HC1. The resulting solution was stirred for an hour and then volatilites were removed under vacuum. The residue was taken in water (1 L) and acidified by 10% HC1 solution (pH 4). The product was then extracted with ethyl acetate (3 x 1 L). the organic phase was then dried and concentrated on rotary evaporator to afford the desired compound 31 (57 g, 24%) as solid.
  • Compound 32 Compound 31 (56 g, 0.1196 mol) was dissolved in 700 mL dry THF and cooled to 0 °C. TBSC1 (36.06 g, 0.2396 mol) was added slowly followed by the addition of imidazole (32.55 g, 0.4786 mol) under an inert atmosphere. The reaction was then stirred at room temperature for 18 hours. Upon completion, the reaction was quenched with ice ( ⁇ 1 kg) and extracted with ethyl acetate (3 x 500 mL).
  • Compound 33 Compound 32 (60 g, 0.1030 mol) was dissolved in 500 mL ethyl acetate and degassed with N 2 for 20 minutes. (10 wt %) Pd on carbon (12 g) was added and the reaction was stirred under an atmosphere of hydrogen for 18 hours. After completion, the mixture was filtered through a bed of celite and washed with ethyl acetate. The filtrate was evaporated under vacuum to afford compound 33 (19 g, 46%) that was pure enough to use in the next synthetic sequence.
  • Compound 34 Compound 33 (8.2 g, 0.0199 mol) was dissolved in 100 mL dry DCM and cooled to 0 °C. TEA (22.14 mL, 0.1592 mol) was added under an inert atmosphere. After stirring the mixture for 5 minutes, mesyl chloride (4.6 mL, 0.059 mol) was added drop wise and the reaction was stirred further for 3 hours. After completion of the reaction, the mixture was quenched with ice (-200 g) and extracted with DCM (3 x 75 mL).
  • reaction progress was monitored by 1H NMR. After completion, the reaction mixture was cooled to 0 °C and quenched by careful addition of saturated NH 4 C1 solution (50 mL) followed by water (200 mL). The aqueous phase was extracted with hexane (3 x 250 mL). The organic layer was dried and solvent removed under vacuum to afford compound 36 (5 g, 94%), which was used without further purification.
  • Compound 39 Compound 37 (2.5 g, 0.00598 mol) was dissolved in 25 mL dry THF and cooled to -40 °C. w-BuLi (1.4 M in hexane 12.9 mL, 0.01794 mol) was added slowly, followed, after a 10 minute interval, by slow addition of HMPA (25 mL). The resulting mixture was maintained for 30 minutes -40 °C under a nitrogen atmosphere. A solution of compound 38 (3.5 g, 1.01196 mol) in 25 mL dry THF was then added drop wise to the cooled reaction mixture. The resulting mixture was warmed to room temperature over 2 hours, then stirred at room temperature for 18 hours.
  • Compound 8 can be synthesized as shown in Scheme 6. Either bromides of compound 58, 60, or 62 can be reacted with ethyl formate to generate terminal-functionalized di-olefin chain.
  • Compound 8 can then be prepared from the diolefin chain compounds using standard chemical reactions.
  • chain length and linker length as well as alkyl groups in ester functionality and substituents on nitrogen atom can be derivatized.
  • Compound 209 Compound 208 (148 mg, 0.181 mmol) was treated with TFA (1.5 mL) in CH 2 CI 2 (6 mL) for 2.5 h. After evaporation and co-evaporation with toluene gave the compound 209 (154 mg, quant.). Molecular weight for C 43 H 8 oN0 6 (M+H) + Calc. 706.5980, Found 706.5.
  • reaction was then warmed to ambient temperature and stirred for 10 hours. After completion of reaction, the mixture was quenched with crushed ice ( ⁇ 2kg) and extracted with ethyl acetate
  • 1, 17-bis-benzyloxy-heptadecan-9-ol (242): To freshly activated Mg turnings (24.08g, 1.003mol) was added 200mL anhydrous THF, followed by the addition of pinch of iodine into the mixture under inert atmosphere. After initiation of the Grignard formation a solution of Compound 241 (150g, 0.5016mol) in 1 L of dry THF was added slowly controlling the exothermic reaction. After complete addition, the reaction was heated to reflux for 1 hour, then cooled to room temperature. Methyl formate (60.24g, 1.0033mol) was then added slowly and reaction was continued for 2 hours.
  • the reaction mixture was then diluted with CH 2 CI 2 (40 mL) and washed with saturated NaHC0 3 (50 mL), water (60 mL) and brine (60 mL). The combined organic layers were dried over anhydrous Na 2 S0 4 and solvents were removed in vacuo.
  • the crude product thus obtained was purified by Combiflash Rf purification system (40 g silicagel, 0- 10 % MeOH in CH 2 C1 2 ) to afford the pure product 246 (0.35 g, 53%) as a colorless oil.
  • Di((Z)-non-2-en-l-yl) 9-hydroxyheptadecanedioate (247) The silyl protected diester 246 (0.3 g, 0.44 mmol) was dissolved in 1 M solution of TBAF in THF (6 mL) and the solution was kept at 40 °C for two days. The reaction mixture was diluted with water (60 mL) and extracted with ether (2 x 50 mL). The combined organic layers were concentrated and the thus obtained crude product was purified by column to isolate the pure product (0.097 g, 39%).
  • the following shorter route was used for the synthesis of analogs of Compound 1 of the present invention
  • the commercial 9-bromonon-l-ene 248 was treated with magnesium to form the corresponding Grignard reagent which was reacted with ethylformate to give the corresponding adduct 249 which on treatment with bromobutyryl chloride to provide the bromoester 250.
  • the bromoester 250 on treatment with Ru0 4 provided the diacid 251.
  • the bromodiacid 251 on treatment with dimethylamine provided the amino diacid 252.
  • the diacid 252 on treatment with oxalyl chloride in the presence of DMF provided the diacid chlorides 253.
  • the lipids 254a-n were synthesized by treating the acid Chloride 253 with respective alcohols.
  • the Bromoacid 251 (2 mmol) is dissolved in 2M solution of dimethylamine in THF (20 mL) and to it 1 g of anhudrous K 2 C0 3 was added and the mixture was heated in a pressure bottle at 50 °C overnight.
  • the TLC showed the completion of the reaction.
  • the reaction mixture was acidified with acetic acid and diluted with water (100 mL) and extracted with dichloromethane (2 x 60 mL). The combined organic layers were concentrated dried and used as such in the next reaction. MW calcd for C 23 H4 3 N0 6 429.59; Found 430.6 (MH) + .
  • the diacid 252 is converted to the corresponding diacid chloride 253 by treating it with oxalyl chloride in dichloromethane in the presence of catalytic DMF and the crude acid chloride obtained after the concentration of the reaction mixture was used as such for the coupling with different alcohols.
  • Di((Z)-non-2-en-l-yl) 9-hydroxyheptadecanedioate (9) The silyl protected diester 8 (0.3 g, 0.44 mmol) was dissolved in 1 M solution of TBAF in THF (6 mL) and the solution was kept at 40 °C for two days after which the TLC showed the completion of the reaction. The reaction mixture was diluted with water (60 mL) and extracted with ether (2 x 50 mL). The combined organic layers were concentrated and the thus obtained crude product was purified by column to isolate the pure product (0.097 g, 39%).
  • the following shorter route was used for the synthesis of the di((Z)-non- 2-en-l-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate.
  • the commercial 9- bromonon-l-ene 10 was treated with magnesium to form the corresponding Grignard reagent which was reacted with ethylformate to give the corresponding adduct 11 which on treatment with bromobutyryl chloride to provide the bromoester 12.
  • the bromoester 12 ontreatment with Ru0 4 provided the diacid 13.
  • the bromodiacid 13 on treatment with dimethylamine provided the amino diacid 14.
  • the aminodiacid 14 on coupling with the alcohol 15 provided the product in good yields.
  • Alcohol 502 The compound 501 (10.25 g, 21.5 mmol) was dissolved in 75 mL of 80 % acetic acid and stirred at room temperature for 14 h. 10 mL of methanol was added and concentrated, followed by column chromatography (0-50 % ethyl acetate in hexane) yielded the expected product 502 as colorless oil (1.8 g, 82 , R f : 0.3, 30 % ethyl acetate in hexane).
  • R alkyl/aryl
  • n 0-10
  • R alkyl/aryl
  • n 0-10
  • Compound 2 was synthesized from 1 using a procedure analogous to that described in Journal of the Organic Chemistry, 2009, 1473.
  • the amino lipids synthesized in Examples 31 and 32 can be converted to the corresponding quaternary lipids as shown below by treatment with CH 3 C1 in CH 3 CN and CHC1 3 .
  • the cationic lipids described herein are used to formulate liposomes containing the AD- 1661 duplex (shown in the table below) using an in-line mixing method as described in International Publication No. WO 2010/088537, which is incorporated by reference in its entirety.
  • the lipid nanoparticles had the formulation shown in the table below.
  • the siRNA AD-1661 duplex has the sequence shown below.
  • Nf is a 2'F modified nucleobase
  • dT is deoxythymidine
  • s is phosphothioate
  • the lipid nanoparticles was prepared as follows. Cationic lipid, DSPC, cholesterol, and PEG-DMG in the ratio recited in the table above were solubilized in ethanol at a total lipid concentration of 25 mg/niL.
  • the stock solutions should be completely clear and the lipids should be completely solubilized before combining with the siRNA. Therefore, if it was determined appropriate, the stock solutions were heated to completely solubilize the lipids.
  • the individual stock solutions were combined by pumping each solution to a T-junction (i.e., by in-line mixing). Specifically, the ethanol solution (at 5 ml/min, via 0.01 in. PEEK tube) and aqueous buffer solution (at 15 mL/min, via 0.02 in. PEEK tube) were mixed through a T- junction (PEEK Tee body, IDEX).
  • Lipid nanoparticles containing the cationic lipids listed in the table in Example 36 were prepared as described above.
  • FVII Factor VII
  • hepatocytes a prominent protein in the coagulation cascade
  • FVII levels in plasma can be determined by a simple, plate-based colorimetric assay.
  • FVII represents a convenient model for determining siRNA-mediated downregulation of hepatocyte-derived proteins.
  • Test formulations of the lipid nanoparticles prepared in Example 35 were initially assessed for their FVII knockdown in female 7-9 week old, 15-25g, female C57B1/6 mice at 0.1, 0.3, 1.0 and 5.0 mg/kg with 3 mice per treatment group. All studies included animals receiving either phosphate-buffered saline (PBS, control group) or a benchmark formulation. Formulations were diluted to the appropriate concentration in PBS immediately prior to testing. Mice were weighed and the appropriate dosing volumes calculated (10 ⁇ /g body weight). Test and benchmark formulations as well as PBS (for control animals) were administered intravenously via the lateral tail vein.
  • PBS phosphate-buffered saline
  • Plasma FVII levels were quantified and ED 50 values (dose resulting in a 50% reduction in plasma FVII levels compared to control animals) were calculated using a standard curve generated from a pooled sample of serum from control animals. Those formulations of interest showing high levels of FVII knockdown (ED 50 « 0.1 mg/kg) were re-tested in independent studies at a lower dose range to confirm potency and establish ED 50 levels.
  • the following table shows ED 50 values for some of the cationic lipids described herein. Two asterisks (**) indicates an ED 50 value between 0.001 and 0.10. One asterisk (*) indicates an ED 50 value greater than 0.10.
  • Example 37 Hydrophobicity and Stability
  • the logP values for the biodegrabable cationic lipids listed in the table below were calculated using the software available at http://www.molinspiration.com/services/logp.html from Molinspiration Cheminformatics of Slovensky Grob, Slovak Republic.
  • the HPLC retention time for each biodegradable cationic lipid was measured in lipid nanoparticles prepared from them.
  • the lipid nanoparticles were prepared as described in Example 35 using AD- 1661 as the payload.
  • the retention times are reported in the table below relative to the retention time for cholesterol.
  • HPLC buffer used was a mixture of two solutions (Solution #1 and Solution #2).
  • Solution #2 80% methanol / 20% isopropanol
  • the ratios of the two solutions in the mixture changed over time as indicated in the table below.
  • the size of the lipid nanoparticles was measured before and after undergoing dialysis overnight. In general, greater changes in lipid nanoparticle size are indicative of lesser stability.
  • Dynamic laser light scattering was used to determine the lipid nanoparticle size (expressed as the intensity weighted diameter) with a Zetasizer (Malvern Instruments, Inc. of Westborough, MA). All measurements were made at 532 nm wavelength at the scattering angle of 173° using normal resolution mode as the analysis model. The results of these experiments are provided in the table below.

Abstract

The present invention relates to a cationic lipid having one or more biodegradable groups located in a lipidic moiety (e.g., a hydrophobic chain) of the cationic lipid. These cationic lipids may be incorporated into a lipid particle for delivering an active agent, such as a nucleic acid. The invention also relates to lipid particles comprising a neutral lipid, a lipid capable of reducing aggregation, a cationic lipid of the present invention, and optionally, a sterol. The lipid particle may further include a therapeutic agent such as a nucleic acid.

Description

BIODEGRADABLE LIPIDS FOR THE DELIVERY OF ACTIVE AGENTS
This application claims the benefit of U.S. Provisional Application No. 61/568,133, filed December 7, 2011, and U.S. Provisional Application No. 61/623,274, filed April 12, 2012, both of which are hereby incorporated by reference.
Technical Field
The present invention relates to biodegradable lipids and to their use for the delivery of active agents such as nucleic acids.
Background
Therapeutic nucleic acids include, e.g., small interfering RNA (siRNA), micro RNA (miRNA), antisense oligonucleotides, ribozymes, plasmids, immune stimulating nucleic acids, antisense, antagomir, antimir, microRNA mimic, supermir, Ul adaptor, and aptamer. In the case of siRNA or miRNA, these nucleic acids can down-regulate intracellular levels of specific proteins through a process termed RNA interference (RNAi). The therapeutic applications of RNAi are extremely broad, since siRNA and miRNA constructs can be synthesized with any nucleotide sequence directed against a target protein. To date, siRNA constructs have shown the ability to specifically down-regulate target proteins in both in vitro and in vivo models. In addition, siRNA constructs are currently being evaluated in clinical studies.
However, two problems currently faced by siRNA or miRNA constructs are, first, their susceptibility to nuclease digestion in plasma and, second, their limited ability to gain access to the intracellular compartment where they can bind the protein RISC when administered systemically as the free siRNA or miRNA. Lipid nanoparticles formed from cationic lipids with other lipid components, such as cholesterol and PEG lipids, and oligonucleotides (such as siRNA and miRNA) have been used to facilitate the cellular uptake of the oligonucleotides. There remains a need for improved cationic lipids and lipid nanoparticles for the delivery of oligonucleotides. Preferably, these lipid nanoparticles would provide high drug:lipid ratios, protect the nucleic acid from degradation and clearance in serum, be suitable for systemic delivery, and provide intracellular delivery of the nucleic acid. In addition, these lipid-nucleic acid particles should be well-tolerated and provide an adequate therapeutic index, such that patient treatment at an effective dose of the nucleic acid is not associated with significant toxicity and/or risk to the patient.
Summary
The present invention relates to a cationic lipid and PEG lipid suitable for forming nucleic acid-lipid particles. Each of the cationic and PEG lipids of the present invention includes one or more biodegradable groups. The biodegradable groups are located in a lipidic moiety (e.g., a hydrophobic chain) of the cationic or PEG lipid. These cationic and PEG lipids may be incorporated into a lipid particle for delivering an active agent, such as a nucleic acid (e.g., an siRNA). The incorporation of the biodegradable group(s) into the lipid results in faster metabolism and removal of the lipid from the body following delivery of the active agent to a target area. As a result, these lipids have lower toxicity than similar lipids without the biodegradable groups.
In one embodiment, the cationic lipid is a compound of formula (I), which has a branched alkyl at the alpha position adjacent to the biodegradable group (between the biodegradable group and the teriary carbon):
Figure imgf000003_0001
Formula (I) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein R' is absent, hydrogen, or alkyl (e.g., C C4 alkyl); with respect to R 1 and R 2 ,
(i) R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R10;
(ii) R 1 and R 2 , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring; or
(iii) one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl (e.g., a 6-member ring) with (a) the adjacent nitrogen atom and (b) the (R)a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR3R4)-; each occurrence of R3 and R4 are, independently H, halogen, OH, alkyl, alkoxy, -NH2, R10, alkylamino, or dialkylamino (in one preferred embodiment, each occurrence of R3 and R4 are, independently H or CrC4 alkyl); each occurrence of R10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein (i) the PEG or polymer is linear or branched, (ii) the PEG or polymer is polymerized by n subunits, (iii) n is a number- averaged degree of polymerization between 10 and 200 units, and (iv) wherein the compound of formula has at most two R10 groups (preferably at most one R10 group); the dashed line to Q is absent or a bond; when the dashed line to Q is absent then Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0- , -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, - OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-; or when the dashed line to Q is a bond then (i) b is 0 and (ii) Q and the tertiary carbon adjacent to it (C*) form a substituted or unsubstituted, mono- or bi-cyclic heterocyclic group having from 5 to 10 ring atoms (e.g., the heteroatoms in the heterocyclic group are selected from O and S, preferably O); each occurrence of R5 is, independently, H or alkyl (e.g. CrC4 alkyl);
X and Y are each, independently, alkylene or alkenylene (e.g., C4 to C2o alkylene or C4 to C2o alkenylene);
1 2
M and are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - 1
OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000005_0001
(wherein R11 is a C2-
Cg alkyl or alkenyl)); each occurrence of Rz is, independently, Q-Cg alkyl (e.g., methyl, ethyl, isopropyl, n- butyl, n-pentyl, or n-hexyl); a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3; and
1 2
Z and Z are each, independently, Cg-C14 alkyl or Cg-C14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a 1 2 double bond which is between the double bond and the terminus of Z or Z (e.g.,
Figure imgf000006_0001
1 2
The R'R R N-(R)a-Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment,
R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
1 2
In one embodiment, R and R are both alkyl (e.g., methyl).
In a further embodiment, a is 3. In another embodiment, b is 0.
In a further embodiment, a is 3, b is 0 and R is -CH2-. In yet a further embodiment, a is 3,
1 2
b is 0, R is -CH2- and Q is -C(0)0-. In another embodiment, R and R are methyl, a is 3, b is 0, R is -CH2- and Q is -C(0)0-.
In another embodiment, X and Y are each, independently -(CH2)n- wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)6-. In another embodiment, X and Y are -(CH2)7-. In yet another embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
1 2
In further embodiments, M and M are each, independently, -OC(O)- or -C(0)0-. For
1 2
example, in one embodiment, M and M are each -C(0)0-.
In another embodiment, the cationic lipid is a compound of formula (II), which has a branched alkyl at the alpha position adjacent to the biodegradable group (between the
1 2
biodegradable group and the terminus of the tail, i.e., Z o Z ):
Figure imgf000007_0001
Formula (II) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein R' is absent, hydrogen, or alkyl (e.g., C C4 alkyl); with respect to R 1 and R 2 ,
(i) R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R10;
(ii) R 1 and R 2 , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring; or
(iii) one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl (e.g., a 6-member ring) with (a) the adjacent nitrogen atom and (b) the (R)a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR3R4)-; each occurrence of R3 and R4 are, independently H, halogen, OH, alkyl, alkoxy, -NH2, R10, alkylamino, or dialkylamino (in one preferred embodiment, each occurrence of R3 and R4 are, independently H or CrC4 alkyl); each occurrence of R10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein (i) the PEG or polymer is linear or branched, (ii) the PEG or polymer is polymerized by n subunits, (iii) n is a number- averaged degree of polymerization between 10 and 200 units, and (iv) wherein the compound of formula has at most two R10 groups (preferably at most one R10 group); the dashed line to Q is absent or a bond; when the dashed line to Q is absent then Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0- , -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, - OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-; or when the dashed line to Q is a bond then (i) b is 0 and (ii) Q and the tertiary carbon adjacent to it (C*) form a substituted or unsubstituted, mono- or bi-cyclic heterocyclic group having from 5 to 10 ring atoms (e.g., the heteroatoms in the heterocyclic group are selected from O and S, preferably O); each occurrence of R5 is, independently, H or alkyl;
X and Y are each, independently, alkylene (e.g., C6-Cg alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
Figure imgf000008_0001
alpha position to the M
1 2
M and are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, -
OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000008_0002
(wherein R11 is a C2-
Cg alkyl or alkenyl)); each occurrence of Rz is, independently, Ci-Cg alkyl (e.g., methyl, ethyl, isopropyl); a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3; and
Z 1 and Z 2 are each, independently, C8-C14 alkyl or C8-C14 alkenyl, wherein (i) the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
Figure imgf000009_0001
and (ii) the terminus of at least one of Z and Z2 is separated from the group
M 1 or M 2 by at least 8 carbon atoms.
In another embodiment, X and Y are each, independently -(CH2)n- wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)6-. In another embodiment, X and Y are -(CH2) -. In yet another embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
1 2
The R'R R N-(R)a-Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
In another embodiment, the cationic lipid is a compound of formula (III), which has a branching point at a position that is 2-6 carbon atoms (i.e., at the beta (β), gamma (γ), delta (δ), epsilon (ε) or zeta position^)) adjacent to the biodegradable group (between the biodegradable group and the terminus of the tail, i.e., Z 1 or Z 2 ):
Figure imgf000009_0002
Formula (III) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R', R1, R2, R, R3, R4, R10, Q, R5, M1, M2, Rz, a, and b are defined as in formula (I);
L 1 and 1 2 are each, independently, C Cs alkylene or C2-C5 alkenylene;
X and Y are each, independently, alkylene (e.g., C4 to C2o alkylene or C6-Cg alkylene) or alkenylene (e.g., C4 to C2o alkenylene); and
Z 1 and Z 2 are each, independently, C8-C14 alkyl or C8-C14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
Figure imgf000010_0001
and with the proviso that the terminus of at least one of Z and Z2 is separated from the group M 1 or M 2 by at least 8 carbon atoms.
In one embodiment, L 1 and L2 are each -CH2-. In another embodiment, L 1 and L2 are each -(CH2)2-. In one embodiment, L 1 and L2 are each -(CH 1
2)3-. In yet another embodiment, L
2 1 2
and L are each -(CH2)4-. In yet another embodiment, L and L are each -(CH2)5-. In yet another embodiment, L 1 and L2 are each -CH2-CH=CH-. In a preferred embodiment, L 1 and L2 are each -CH2- or -(CH2)2.
In one embodiment, X and Y are each, independently -(CH2)n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2) -. In another exemplary embodiment, X and Y are -(CH2)8-. In yet another exemplary embodiment, X and Y are -(CH2)cr.
1 2
The R'R R N-(R)a-Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-. In another embodiment, the cationic lipid is a compound of formula (IIIA), which has a branching point at a position that is 2-6 carbon atoms (i.e., at the beta (β), gamma (γ), delta (δ), epsilon (ε) or zeta position^)) from the biodegradable groups M1 and M2 (i.e., between the biodegradable group and the terminus of the tail, i.e., Z 1 or Z 2 ):
Figure imgf000011_0001
Formula (IIIA) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R', R1, R2, R, R3, R4, R10, Q, R5, M1, M2, a, and b are defined as in formula (I); each Rz is, independently, Q-Cg alkyl (e.g., C3-C6 alkyl or C2-C3 alkyl);
L 1 and V 2 are each, independently, Q-Cs alkylene (e.g., C2-C3 alkylene) or C2-C5 alkenylene;
X and Y are each, independently, alkylene (e.g., C4 to C20 alkylene or C7-C9 alkylene) or alkenylene (e.g., C4 to C20 alkenylene or C7-C9 alkenylene); and
Z 1 and Z 2 are each, independently, Q-Cg alkyl (e.g., Ci-C6 alkyl, such as Q, C3 or C5 alkyl) or C2-Cg alkenyl (such as C2-C6 alkenyl); wherein said cationic lipid is not one selected from:
Figure imgf000011_0002
Figure imgf000012_0001
In one embodiment, L 1 and L2 are each -(CH2)2-. In another embodiment, L 1 and L2 are each -(CH2)3-. In one embodiment, X and Y are each, independently -(CH2)n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, 4 to 12 or 7-9. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)7-. In yet another exemplary embodiment, X and Y are -(CH2)9.
In one preferred embodiment, M 1 and M2 are -C(0)0- (where the carbonyl group in M 1 and M 2 is bound to the variable X, and the oxygen atom in M 1 and M2 is bound to the variable L 1 and L2).
1 2
The R'R R N-(R)a-Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
In one preferred embodiment, Z 1 and Z 2 are branched alkyl or branched alkenyl groups.
In one embodiment of formula (IIIA), Z1, Z2, and each Rz are C3-C8 alkyl (such as a C3- C6 alkyl). In another embodiment of formula (IIIA), Z1, Z2, and each Rz are C3-Cg branched alkyl (such as a C3-C6 branched alkyl). In yet another embodiment of formula (IIIA), Z 1 , Z 2 , and each Rz are C3-C8 straight alkyl (such as a C3-C6 straight alkyl).
In one embodiment of formula (IIIA), the branching point is at the second position (the β- position) from the biodegradable groups M1 and M2 in each tail. Z1, Z2, and each Rz can be C3- Cg alkyl (e.g., a C3-C6 alkyl), such as a C3-Cg branched alkyl (e.g., a C3-C6 branched alkyl) or a
C traight alkyl (e.g., a C3-C6 straight alkyl). In one preferred embodiment, M 1 and M 2 3-C8 s are -
C(0)0- (where the carbonyl group in M 1 and M 2 is bound to the variable X, and the oxygen atom in M 1 and M2 is bound to the variable L 1 and/or L2 ).
In one embodiment of formula (IIIA), the branching point is at the third position (the γ- position) from the biodegradable groups M1 and M2 in each tail. Z1, Z2, and each Rz can be C3- C8 alkyl (e.g., a C3-C6 alkyl), such as a C3-C8 branched alkyl (e.g., a C3-C6 branched alkyl) or a
C3-Cg straight alkyl (e.g., a C3-C6 straight alkyl). In one preferred embodiment, M 1 and M 2 are -
C(0)0- (where the carbonyl group in M 1 and M 2 is bound to the variable X, and the oxygen atom in M 1 and M2 is bound to the variable L 1 and/or L2 ). In one embodiment of formula (IIIA), the branching point is at the third position (the γ- position) from the biodegradable groups M 1 and M 2 in each tail.
In another embodiment of formula (IIIA), M 1 and/or M 2 are not -0(C(0)- (where the oxygen atom in M 1 and/or M2 is bound to the variable X, and the carbonyl in M 1 and/or M2 is bound to the variable L1 and/or L2). In yet another embodiment of formula (IIIA), Z1, Z2, and Rz are not C3-Q0 cyclo alkyl (Ci-C6 alkyl).
In another embodiment, the cationic lipid is a compound of formula (IV), which has a branching point at a position that is 2-6 carbon atoms (i.e., at beta (β), gamma (γ), delta (δ), epsilon (ε) or zeta position^)) adjacent to the biodegradable group (between the biodegradable group and the terminus of the tail i.e., Z 1 or Z 2 ):
Figure imgf000014_0001
Formula (IV)
or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R', R1, R2, R, R3, R4, R10, Q, R5, M1, M2, Rz, a, and b are defined as in formula (I);
L 1 and L 2 and are each, independently, C Cs alkylene or C2-C5 alkenylene;
X and Y are each, independently, alkylene or alkenylene (e.g., C12-C2o alkylene or C12- C2o alkenylene); and
each occurrence of Z is independently Q-C4 alkyl (preferably, methyl).
For example, in one embodiment, -L1-C(Z)3 is -CH2C(CH3)3. In another embodiment, - ΐΛ^Ζ)3 is -CH2CH2C(CH3)3.
In one embodiment, the total carbon atom content of each tail (e.g., -X-M1-L1-C(Z) or -
Y-M 2 -L 2 -C(Z) ) is from about 17 to about 26. For example, the total carbon atom content can be from about 19 to about 26 or from about 21 to about 26.
In another embodiment, X and Y are each, independently -(CH2)n- wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)6-. In another embodiment, X and Y are -(CH2) -. In yet another embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
In one embodiment, the cationic lipid is a compound of formula (V), which has an alkoxy or thioalkoxy (i.e., -S-alkyl) group substitution on at least one tail:
Figure imgf000015_0001
Formula (V) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R', R1, R2, R, R3, R4, R10, Q, R5, M1, M2, a, and b are defined as in formula (I);
X and Y are each, independently, alkylene (e.g., C6-C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
alpha position to the M or M2 group (e.g.,
Figure imgf000015_0002
Z 1 and Z 2 are each, independently, Cg-C14 alkyl or Cg-C14 alkenyl, wherein (i) the Cg-C14 alkyl or Cs-C14 alkenyl of at least one of Z 1 and Z 2 is substituted by one or more alkoxy (e.g., a CrC4 alkoxy such as -OCH3) or thioalkoxy (e.g., a CrC4 thioalkoxy such as -SCH3) groups, and (ii) the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2
(e.g.,
Figure imgf000015_0003
In one embodiment, the alkoxy substitution on Z 1 and/or Z 2 is at the beta position from the M1 and/or M2 group. In another embodiment, X and Y are each, independently -(CH2)n- wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)6-. In another embodiment, X and Y are -(CH2)7-. In yet another embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
1 2
The R'R R N-(R)a-Q-(R)t>- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
In one embodiment, the cationic lipid is a compound of formula (VIA), which has one or more fluoro substituents on at least one tail at a position that is either alpha to a double bond or alpha to a biodegradable group:
Figure imgf000016_0001
Formula (VIA) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R 1 , R 2 , R, a, and b are as defined with respect to formula (I);
Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0-, -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, - S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, -OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0- , -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-;
R' is absent, hydrogen, or alkyl (e.g., C C4 alkyl); and each of R9 and R10 are independently C12-C24 alkyl (e.g., C12-C2o alkyl), C12-C24 alkenyl (e.g., C12-C2o alkenyl), or C12-C24 alkoxy (e.g., C12-C20 alkoxy) (a) having one or more biodegradable groups and (b) optionally substituted with one or more fluorine atoms at a position which is (i) alpha to a biodegradable group and between the biodegradable group and the tertiary carbon atom marked with an asterisk (*), or (ii) alpha to a carbon-carbon double bond and between the double bond and the terminus of the R9 or R10 group; each biodegradable group independently interrupts the C12-C24 alkyl, alkenyl, or alkoxy group or is substituted at the terminus of the C12-C24 alkyl, alkenyl, or alkoxy group,
wherein
at least one of R9 and R10 contains a fluoro group;
the compound does not contain the following moiety:
Figure imgf000017_0001
wherein— is an optional bond; and
(iii) the terminus of R9 and R10 is separated from the tertiary carbon atom marked with an asterisk (*) by a chain of 8 or more atoms (e.g., 12 or 14 or more atoms).
In one preferred embodiment, the terminus of R9 and R10 is separated from the tertiary carbon atom marked with an asterisk (*) by a chain of 18-22 carbon atoms (e.g., 18-20 carbon atoms).
In another embodiment, the terminus of the R9 and/or R10 has the formula -C(0)0-CF3.
In another embodiment, the cationic lipid is a compound of formula (VIB), which has one or more fluoro substituents on at least one tail at a position that is either alpha to a double bond or alpha to a biodegradable group:
Figure imgf000017_0002
Formula (VIB) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R' , R1, R2, R, R3, R4, R10, Q, R5, M1, M2, a, and b are defined as in formula (I);
X and Y are each, independently, alkylene (e.g., C6-C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
Figure imgf000018_0001
alpha position to the M or M group (e.g., and
1 2
Z and Z are each independently, Cg-C14 alkyl or Cg-C14 alkenyl, wherein said Cg-C14 alkenyl is optionally substituted by one or more fluorine atoms at a position that is alpha to a
double bo
Figure imgf000018_0002
,
1 2
wherein at least one of X, Y, Z , and Z contains a fluorine atom.
1 2
In one embodiment, at least one of Z and Z is substituted by two fluoro groups at a position that is either alpha to a double bond or alpha to a biodegradable group. In one
1 2
embodiment, at least one of Z and Z has a terminal -CF3 group at a position that is alpha to a
1 2
biodegradable group (i.e., at least one of Z and Z terminates with an -C(0)OCF3 group).
1 2
For example, at least one of Z and Z may include one or more of the following moieties:
Figure imgf000018_0003
In one embodiment, X and Y are each, independently -(CH2)n wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2) -. In another exemplary embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
1 2
The R'R R N-(R)a-Q-(R)b- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
In one embodiment, the cationic lipid is a compound of formula (VII), which has an acetal group as a biodegradable group in at least one tail:
Figure imgf000019_0001
Formula (VII) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
R', R1, R2, R, R3, R4, R10, Q, R5, a, and b are defined as in formula (I);
X and Y are each, independently, alkylene (e.g., C6-C8 alkylene) or alkenylene, wherein the alkylene or alkenylene group is optionally substituted with one or two fluorine atoms at the
Figure imgf000019_0002
alpha position to the M or M group (e.g.,
M 1 and 2 are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - 1
OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000020_0001
(wherein R11 is a C4-
Cio alkyl or C4-C10 alkenyl)); 1
with the proviso that at least one of M 1 and M 2
Figure imgf000020_0002
; and
Z 1 and Z 2 are each, independently, C4-C14 alkyl or C4-C14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 (e.g.,
Figure imgf000020_0003
In one embodiment, each of M 1 and M 2
Figure imgf000020_0004
.
In another embodiment, X and Y are each, independently -(CH2)n- wherein n is 4 to 20, e.g., 4 to 18, 4 to 16, or 4 to 12. In one embodiment, n is 4, 5, 6, 7, 8, 9, or 10. In one exemplary embodiment, X and Y are -(CH2)6-. In another embodiment, X and Y are -(CH2)7-. In yet another embodiment, X and Y are -(CH2)9-. In yet another embodiment, X and Y are -(CH2)8-.
1 2
The R'R R N-(R)a-Q-(R)t>- group can be any of the head groups described herein, including those shown in Table 1 below, and salts thereof. In one preferred embodiment, R'R1R2N-(R)a-Q-(R)b- is (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N- (CH2)2-OC(0)-NH-, or (CH3)2N-(CH2)3-C(CH3)=N-0-.
In another embodiment, the present invention relates to a cationic lipid or a salt thereof having:
(i) a central carbon atom, (ii) a nitrogen containing head group directly bound to the central carbon atom, and
(iii) two hydrophobic tails directly bound to the central carbon atom, wherein each hydrophobic tail is of the formula -Re-M-Rf where Re is a C4-C14 alkyl or alkenyl, M is a biodegradable group, and R is a branched alkyl or alkenyl (e.g., a Cio-C2o alkyl or Cio-C2o alkenyl), such that (i) the chain length of -Re-M-Rf is at most 20 atoms (i.e. the total length of the tail from the first carbon atom after the central carbon atom to a terminus of the tail is at most 20), and (ii) the group -Re-M-Rf has at least 20 carbon atoms (e.g., at least 21 atoms). Optionally, the alkyl or alkenyl group in Re may be substituted ith one or two fluorine atoms at
Figure imgf000021_0001
the alpha position to the M or M2 group (e.g., Also, optionally, the alkenyl group in R may be substituted with one or two fluorine atoms at the alpha position to a double
bond which is between the double bond and the terminus of R (e.g.,
Figure imgf000021_0002
).
In one embodiment, the cationic lipid of the present invention (such as of formulas I- VII) has assymetrical hydrophobic groups (i.e., the two hydrophobic groups have different chemical formulas). For example, the cationic lipid can have the formula: 3
Figure imgf000021_0003
Formula (VIII) or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), wherein
G is branched or unbranched C3-C15 alkyl, alkenyl or alkynyl (e.g., a n-Cg alkyl n-Cg alkyl, or n-C10 alkyl); R is a branched or unbranched alkylene or alkenylene (e.g., C6-C20 alkylene or C6-C20 alkenylene such as C12-C2o alkylene or C12-C2o alkenylene);
Mi is a biodegradable group (e.g., -OC(O)-, -C(0)0-, -SC(O)-, -C(0)S-, -OC(S)-, - C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, -OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -
OC(0)(CR3R4)C(0)-, or
Figure imgf000022_0001
(wherein R11 is a C2-C8 alkyl or alkenyl)); R3 and R4 are defined as in formula (I); each occurrence of R5 is, independently, H or alkyl (e.g., C1-C4 alkyl);
Primary Group
R is branched or unbranched C3-C15 alkyl, alkenyl or alkynyl;
comprises a protonatable group having a pKa of from about 4 to about 13, more preferably from about 5 to about 8 (e.g. from about 5 to about 7, or from about 5 to about 6.5, or from about 5.5 to about 6.5, or from about 6 to about 6.5).
In one embodiment, the primary group includes (i) a head group, and (ii) a central moiety (e.g., a central carbon atom) to which both the hydrophobic tails are directly bonded. Representative central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group.
Primary Group
Represent ude, but are not limited to,
Figure imgf000022_0002
Figure imgf000022_0003
Figure imgf000023_0001
: where n is 0-6.
Representative asymmetrical cationic lipids include:
Figure imgf000023_0002
wherein w is 0, 1, 2, or 3; and x and y are each independently 1, 2, 3, 4, 5, 6, or 7.
In a preferred embodiment of the aforementioned biodegradable cationic lipids, the biodegradable cationic lipid has a logP value of at least 10.1 (as calculated by the software available at http://www.molinspiration.com/services/logp.html from Molinspiration Cheminformatics of Slovensky Grob, Slovak Republic). More preferably, the logP value is at least 10.2 or 10.3.
In another preferred embodiment of the aforementioned biodegradable cationic lipids, the biodegradable cationic lipid in the lipid nanoparticle has a HPLC retention time (relative to the retention time of cholesterol in the lipid nanoparticle), hereafter referred to as tiipi(j - tchol, of at least 1.4. (The HPLC parameters are provided in the examples below. Unless otherwise specified, the formulation of the lipid nanoparticle used is that described in Example 31). More preferably, the tuPid - tchoi value is at least 1.75, 2.0, or 2.25.
In another embodiment, the biodegradable cationic lipid of the present invention is not one selected from:
Figure imgf000024_0001
Figure imgf000025_0001
m = 1 -6; n = 0-3 1
R-i = R2 = Me, Et, iPr etc.
Figure imgf000025_0002
where m and n are integers, and m + n
Figure imgf000025_0003
where m and n are integers, and m + n
Figure imgf000025_0004
where m and n are integers, and m + n
Figure imgf000025_0005
where m and n are integers, and m + n In yet another embodiment, the biodegradable cationic lipid is not one selected from those disclosed in International Publication No. WO 2011/153493 and U.S. Patent Publication No. 2012/0027803, both of which are hereby incorporated by reference.
Yet another embodiment is a biodegradable cationic lipid having (i) a logP value of at least 10.1 and/or a tiipi(j - tchol, of at least 1.4, and (2) one or more biodegradable groups (such as an ester group) located in the mid- or distal section of a lipidic moiety (e.g., a hydrophobic chain) of the cationic lipid, with the proviso that the compound is not selected from
Figure imgf000026_0001
In another embodiment, the biodegradable cationic lipid is not one selected from those disclosed in International Publication No. WO 2011/153493 and U.S. Patent Publication No. 2012/0027803, both of which are hereby incorporated by reference. The incorporation of the biodegradable group(s) into the cationic lipid results in faster metabolism and removal of the cationic lipid from the body following delivery of the active pharmaceutical ingredient to a target area. In a preferred embodiment, the cationic lipid includes a branched alkyl or branched alkenyl group in its biodegradable group(s). In another preferred embodiment, the cationic lipd has a logP of at least 10.2 or 10.3. In yet another preferred embodiment, the cationic lipid has a tiipi(j - tchoh °f at least 1.75, 2.0, or 2.25. The cationic lipid preferably has a pKa of from about 4 to about 7 (such as 6.0 to 6.5).
In one embodiment, the cationic lipid having a logP value of at least 10.1 and/or a tuPid - tchoh °f at least 1.4 comprises (a) a head group (preferably a nitrogen containing head group, such as the head groups described herein), (b) at least two hydrophobic tails, each of the formula - (hydrophobic chain) -(biodegradable group)- (hydrophobic chain), and (c) a linker group (for instance, a single central carbon atom) which is bound to the head group and the hydrophobic tails. The cationic lipid preferably has one, two, three, four or more of the properties listed below:
(i) a pKa of from about 4 to about 7 (such as 6.0 to 6.5);
(ii) in at least one hydrophobic tail (and preferably all hydrophobic tails), the biodegradable group is separated from the terminus of the hydrophobic tail by from about 6 to about 12 carbon atoms (for instance, 6 to 8 carbon atoms or 8 to 12 carbon atoms),
(iii) for at least one hydrophobic tail (and preferably all hydrophobic tails), the chain length from the linker group to the terminus of the hydrophobic tail is at most 21 (e.g., at most 20, or from about 17 to about 21, from about 18 to about 20, or from about 16 to about 18) (The atom(s) in the linker group are not counted when calculating the chain length.);
(iv) for at least one hydrophobic tail (and preferably all hydrophobic tails), the total number of carbon atoms in the hydrophobic tail is from about 17 to about 26 (such as from about 19 to about 26, or from about 21 to about 26);
(v) for at least one hydrophobic tail (and preferably all hydrophobic tails), the number of carbon atoms between the linker group and the biodegradable group ranges from about 5 to about 10 (for example, 6 to 10, or 7 to 9);
(vi) for at least one hydrophobic tail (and preferably all hydrophobic tails), the total number of carbon atoms between the linker group and the terminus of the hydrophobic tail is from about 15 to about 20 (such as from 16 to 20, 16 to 18, or 18 to 20);
(vii) for at least one hydrophobic tail (and preferably all hydrophobic tails), the total number of carbon atoms between the biodegradable group and the terminus of the hydrophobic tail is from about 12 to about 18 (such as from 13 to 25); (viii) for at least one hydrophobic tail (and preferably all hydrophobic tails), the terminal hydrophobic chain in the hydrophobic tail is a branched alkyl or alkenyl group, for example, where the branching occurs at the α, β, γ, or δ position on the hydrophobic chain relative to the biodegradable group;
(ix) when formulated as a lipid nanoparticle (such as in Example 35), the cationic lipid has an in vivo half life (t1/2) in the liver of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours;
(x) when formulated as a lipid nanoparticle (such as in Example 35), the cationic lipid is eliminated from the liver in mice with a greater than 10-fold reduction in lipid levels relative to Cmax within the first 24 hours post-dose;
(xi) when formulated as a lipid nanoparticle (such as in Example 35), the cationic lipid is eliminated from the spleen in mice with an equal or greater than 10-fold reduction in lipid levels relative to Cmax within the first 168 hours post-dose; and
(xii) when formulated as a lipid nanoparticle (such as in Example 35), the cationic lipid is eliminated from plasma with a terminal plasma half-life (ί1/2β) in rodents and non-human primates of 48 hours or shorter.
The present invention embodies compounds having any combination of some or all of the aforementioned properties. These properties provide a cationic lipid which remains intact until delivery of an active agent, such as a nucleic acid, after which cleavage of the hydrophobic tail occurs in vivo. For instance, the compounds can have all of properties (i) to (viii) (in addition to the logP or tiipi(j - tclloi value). In another embodiment, the compounds have properties (i), (ii), (iii), and (viii). In yet another embodiment, the compounds have properties (i), (ii), (iii), (v), (vi), and (viii).
Another embodiment is a method of preparing a cationic lipid comprising:
(a) designing a cationic lipid having a logP value of at least 10.1 and/or a tiipi(j - tch0i, of at least 1.4, and optionally also having one, two, three, four, or more properties from the list above (i.e., properties (i)-(xii)); and (b) synthesizing the cationic lipid of step (a). The cationic lipid in step (a) may comprises (a) a head group (preferably a nitrogen containing head group, such as the head groups described herein), (b) at least two hydrophobic tails, each of the formula -(hydrophobic chain)- (biodegradable group)-(hydrophobic chain), and (c) a linker group (for instance, a single central carbon atom) which is bound to the head group and the hydrophobic tails. Step (a) may comprise:
(a)(i) preparing one or more cationic lipids having a logP value of at least 10.1 and/or a tiipid - tchoi, of at least 1.4, and optionally also having one, two, three, four, or more properties from the list above (i.e., properties (i)-(xii);
(a)(ii) screening the cationic lipids to determine their efficacy and/or toxicity in lipid nanoparticles; and
(a)(iii) selecting a cationic lipid for synthesis.
Yet another embodiment is a method of designing a cationic lipid comprising:
(a) selecting a cationic lipid having a logP value of at least 10.1 and/or a tiipi(j - tch0i, of at least 1.4, and optionally also having one, two, three, four, or more properties from the list above (i.e., properties (i)-(xii)); and
(b) optionally,
(i) preparing one or more cationic lipids having a logP value of at least 10.1 and/or a tuPid - tchoi, of at least 1.4, and optionally also having one, two, three, four, or more properties from the list above (i.e., properties (i)-(xii);
(ii) screening the cationic lipids to determine their efficacy and/or toxicity in lipid nanoparticles; and
(iii) optionally, selecting a cationic lipid for further development or use. In one embodiment, the PEG lipid has the formula:
Figure imgf000030_0001
Formula (IX) wherein
Gi is branched or unbranched C3-C15 alkyl, alkenyl or alkynyl (e.g., a n-C^ alkyl n-C9 alkyl, or n-C10 alkyl); or Gi is -R12-M R13;
12
R is a branched or unbranched alkylene or alkenylene (e.g., C6-C20 alkylene or C6-C20 alkenylene such as C12-C20 alkylene or Ci2-C2o alkenylene);
Mi is a biodegradable group (e.g., -OC(O)-, -C(0)0-, -SC(O)-, -C(0)S-, -OC(S)-, - C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, -OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -
OC(0)(CR3R4)C(0)-, or
Figure imgf000030_0002
(wherein R11 is a C2-C8 alkyl or alkenyl));
R3 and R4 are defined as in formula (I); each occurrence of R5 is, independently, H or alkyl (e.g., C1-C4 alkyl);
13
R is branched or unbranched C3-C15 alkyl, alkenyl or alkynyl;
Pegylated Primary Group
comprises a PEG moiety, such as
Figure imgf000030_0003
moiety wherein b is an integer from 10 to 1,000 (e.g., 5-100, 10-60, 15-50, or 20-45); RJ is -H, -Rc, or -ORc; and Rc is -H, alkyl, acyl, cycloalkyl, alkenyl, alkynyl, aryl, heteroaryl, or heterocyclyl. In one embodiment, the pegylated primary group includes (i) a head group having a PEG moiety, and (ii) a central moiety (e.g., a central carbon atom) to which both the hydrophobic tails are directly bonded. Representative central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group.
Pegylated Primary Group
's include, but are not limited to,
Figure imgf000031_0001
where b is 10-100 (e.g., 20-50 or 40-50)
Another embodiment of the present invention is a PEG lipid (or a salt thereof) having: (i) a pegylated primary group including a head group which includes a PEG moiety (e.g., having from 10 to 1000 repeating units such as ethoxy units)), and
(iii) one or more hydrophobic tails (preferably, two hydrophobic tails) directly bound to the pegylated primary group, wherein at least one hydrophobic tail is of the formula -Re-M-Rf where Re is a C4-C14 alkyl or alkenyl, M is a biodegradable group, and Rf is a branched alkyl or alkenyl (e.g., a Cio-C2o alkyl or Cio-C2o alkenyl), such that (i) the chain length of -Re-M-Rf is at most 20 atoms (i.e. the total length of the tail from the first carbon atom after the central carbon atom to a terminus of the tail is at most 20), and (ii) the group -Re-M-Rf has at least 20 carbon atoms (e.g., at least 21 atoms). Optionally, the alkyl or alkenyl group in Re may be substituted
with one or two fluorine atoms at the alpha position to the M 1 or M 2 group (e.g.,
Figure imgf000032_0001
). Also, optionally, the alkenyl group in R may be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of R
Figure imgf000032_0002
In one embodiment, the pegylated primary group includes (i) a head group having a PEG moiety, and (ii) a central moiety (e.g., a central carbon atom) to which the hydrophobic tails are directly bound. The PEG moiety may have 5-100, 10-60, 15-50, or 20-45 repeating units. For example, the PEG moiety may have the formula u moiety wherein b is an integer from 10 to 1,000 (e.g., 5-100, 10-60, 15-50, or 20-45); R3 is -H, -Rc, or -ORc; and Rc is -H, alkyl (e.g., CrC4 alkyl), acyl, cycloalkyl, alkenyl, alkynyl, aryl, heteroaryl, or heterocyclyl.
Yet another embodiment is a lipid particle that includes a cationic lipid and/or PEG lipid of the present invention. In one embodiment, the lipid particle includes a cationic lipid of the present invention (e.g., of one of formulas (I)-(VIII)). In another embodiment, the lipid particle includes a PEG lipid of the present invention (e.g., of formula (IX)). In yet another embodiment, the lipid particle includes a cationic lipid of the present invention and a PEG lipid of the present invention.
In a preferred embodiment, the lipid particle includes a neutral lipid, a lipid capable of reducing aggregation, a cationic lipid, and optionally, a sterol (e.g., cholesterol). Suitable neutral lipids include, but are not limited to, distearoylphosphatidylcholine (DSPC), dipalmitoylphosphatidylcholine (DPPC), POPC, DOPE, and SM. Suitable lipids capable of reducing aggregation include, but are not limited to, a PEG lipid, such as PEG-DMA, PEG- DMG, and those of the present invention (e.g., of formula (IX)) or a combination thereof. The lipid particle may further include an active agent (e.g., a therapeutic agent). The active agent can be a nucleic acid such as a plasmid, an immuno stimulatory oligonucleotide, an siRNA, an antisense oligonucleotide, a microRNA, an antagomir, an aptamer, or a ribozyme. In a preferred embodiment, the nucleic acid is a siRNA. In another preferred embodiment, the nucleic acid is a miRNA.
In another embodiment, the lipid particle includes a cationic lipid of the present invention, a neutral lipid and a sterol. The lipid particle may further include an active agent, such as a nucleic acid (e.g., an siRNA or miRNA).
In yet another embodiment, the lipid particle includes a PEG lipid of the present invention, a cationic lipid, a neutral lipid, and a sterol. The lipid particle may further include an active agent, such as a nucleic acid (e.g., an siRNA or miRNA).
The lipid particles described herein may be lipid nanoparticles.
Yet another embodiment of the invention is a pharmaceutical composition which includes a lipid particle of the present invention and a pharmaceutically acceptable carrier.
In one embodiment, the cationic lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
In another embodiment, the PEG lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
In another embodiment, the present invention relates to a method of delivering a nucleic acid molecule comprising administering a nucleic lipid particle comprising (i) the nucleic acid molecule and (ii) a cationic lipid and/or a PEG lipid of the present invention. In one embodiment, the cationic lipid and/or a PEG lipid remains intact until delivery of the nucleic acid molecule after which cleavage of the hydrophobic tail occurs in vivo.
Yet another aspect is a method of modulating the expression of a target gene in a cell by providing to the cell a lipid particle of the present invention. The active agent can be a nucleic acid selected from a plasmid, an immuno stimulatory oligonucleotide, an siRNA, an antisense oligonucleotide, a microRNA, an antagomir, an aptamer, and a ribozyme. In a preferred embodiment, the nucleic acid is a siRNA or miRNA.
Yet another aspect is a method of treating a disease or disorder characterized by the overexpression of a polypeptide in a subject by providing to the subject a pharmaceutical composition of the present invention, wherein the active agent is a nucleic acid selected from an siRNA, a microRNA, and an antisense oligonucleotide, and wherein the siRNA, microRNA, or antisense oligonucleotide includes a polynucleotide that specifically binds to a polynucleotide that encodes the polypeptide, or a complement thereof. In a preferred embodiment, the nucleic acid is a siRNA or miRNA.
Yet another aspect is a method of treating a disease or disorder characterized by underexpression of a polypeptide in a subject by providing to the subject a pharmaceutical composition of the present invention, wherein the active agent is a plasmid that encodes the polypeptide or a functional variant or fragment thereof.
Yet another aspect is a method of inducing an immune response in a subject by providing to the subject a pharmaceutical composition wherein the active agent is an immuno stimulatory oligonucleotide.
Yet another aspect is a transfection agent that includes the composition or lipid particles described above, where the composition or lipid particles include a nucleic acid. The agent, when contacted with cells, can efficiently deliver nucleic acids to the cells. Yet another aspect is a method of delivering a nucleic acid to the interior of a cell, by obtaining or forming a composition or lipid particles described above, and contacting the composition or lipid particles with a cell.
Detailed Description
In one aspect, the present invention relates to a lipid particle that includes a neutral lipid, a lipid capable of reducing aggregation (e.g., a PEG lipid), a cationic lipid, and optionally a sterol. In certain embodiments, the lipid particle further includes an active agent (e.g., a therapeutic agent). Various exemplary embodiments of these lipids, lipid particles and compositions comprising the same, and their use to deliver therapeutic agents and modulate gene and protein expression are described in further detail below.
The Cationic Lipid
In one embodiment, the cationic lipid is a compound of any one of Formulas I- VIII. The following disclosure represents various embodiments of the compounds described above, including the compounds of Formulas I- VIII.
In one embodiment, M 1 and M 2 are each, independently:
-OC(O)-, -C(0)0-, -SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, - C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, - N(R5)C(0)N(R5)-, -OC(0)0-, -OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000035_0001
(wherein R11 is a C2-C8 alkyl or alkenyl).
In another embodiment, M 1 and M 2 are each, independently:
-OC(O)-, -C(0)-0-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -0-C(0)0-, - C(0)N(R5)-, -N(R5)C(0)-, -C(0)S-, -SC(O)-, -C(S)0-,-OC(S)-, -OSi(R5)20-, - C(0)(CR3R4)C(0)0-, or -OC(0)(CR3R4)C(0)-.
In yet another embodiment, M 1 and M 2 are each, independently:
-C(0)-0-, -OC(O)-, -C(R5)=N-, -C(R5)=N-0-, -0-C(0)0-, -C(0)N(R5)-, -C(0)S-, - C(S)0-, -OSi(R5)20-, -C(0)(CR3R4)C(0)0-, or -OC(0)(CR3R4)C(0)-.
In another embodiment, M 1 and M 2 are each -C(0)0-. In one embodiment, R 1 and R 2 are each, individually, optionally substituted alkyl, cycloalkyl, cycloalkylalkyl, or heterocycle. In one embodiment, R 1 is alkyl and R 2 is alkyl, cycloalkyl or cycloalkylalkyl. In one embodiment, R 1 and R 2 are each, individually, alkyl (e.g.,
CrC4 alkyl, such as methyl, ethyl, or isopropyl). In one embodiment, R 1 and R 2 are both methyl.
In another embodiment, R 1 and R 2 , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring ( -methylpiperazinyl). In another
embodiment, one of R1 and R2 is
Figure imgf000036_0001
aforementioned groups and R is hydrogen).
In one embodiment, R' is hydrogen or alkyl. In another embodiment, R' is hydrogen or methyl. In one embodiment, R' is absent. In one embodiment, R' is absent or methyl.
For cationic lipid compounds which contain an atom (e.g., a nitrogen atom) that carries a positive charge, the compound also contains a negatively charged counter ion. The counterion can be any anion, such as an organic or inorganic anion. Suitable examples of anions include, but are not limited to, tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, a-ketoglutarate, a-glycerophosphate, halide (e.g., chloride), sulfate, nitrate, bicarbonate, and carbonate. In one embodiment, the counterion is a halide (e.g., CI).
In one embodiment each R is, independently, -(CR3R4)-, wherein R3 and R4 are each, independently, H or alkyl (e.g., C C4 alkyl). For example, in one embodiment each R is, independently, -(CHR4)-, wherein each R4 is, independently H or alkyl (e.g., CrC4 alkyl). In another embodiment, each R is, independently, -CH2-, -C(CH3)2- or -CH(iPr)- (where iPr is isopropyl). In another embodiment, each R is -CH2-.
In another embodiment R5 is, in each case, hydrogen or methyl. For example, R5 can be, in each case, hydrogen. In one embodiment, Q is absent, -C(0)0-, -OC(O)-, -C(0)N(R5)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -C(R5)=N-0-, -OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-. In one embodiment, Q is -C(0)0-.
In one embodiment, the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R)a-Q- and the tertiary carbon adjacent to it (C*) form the following group:
Figure imgf000037_0001
where n is 1 to 4 (e.g., n is 2).
In one embodiment, the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R)a-Q- and the tertiary carbon adjacent to it form the following group:
Figure imgf000037_0002
where n is 1 to 4 (e.g., n is 2), and R 1 , R 2 , R, a, and b are as defined with respect to formula (I).
In one embodiment, a is 3.
In one embodiment, the dashed line to Q is absent, b is 0 and R'R 1 R 2 N-(R)a-Q- and the tertiary carbon adjacent to it form the following group:
Figure imgf000037_0003
where n is 1 to 4 (e.g., n is 2), and R 1 , R 2 , R, a, and b are as defined with respect to formula (I). In one embodiment, a is 0. For example, the group can be:
Figure imgf000038_0001
In one embodiment, b is 0. In another embodiment, a is 2, 3, or 4 and b is 0. For example, in one embodiment, a is 3 and b is 0. In another embodiment, a is 3, b is 0, and Q is -C(0)0-.
In certain embodiments, the biodegradable group present in the cationic lipid is selected from an ester (e.g., -C(0)0- or -OC(O)-), disulfide (-S-S-), oxime (e.g., -C(H)=N-0- or -O- N=C(H)-), -C(0)-0-, -OC(O)-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -0-C(0)0-, -C(0)N(R5), -N(R5)C(0)-, -C(S)(NR5)-, (NR5)C(S)-, -N(R5)C(0)N(R5)-, -C(0)S-, -SC(O)-, - C(S)0-,-OC(S)-, -OSi(R5)20-, -C(0)(CR3R4)C(0)0-, or -OC(0)(CR3R4)C(0)-.
A suitable cholesterol moiety for the cationic lipids of the present invention (including compounds of formulas I- VI) has the formula:
Figure imgf000038_0002
Additional embodiments include a cationic lipid having a head group, one or more hydrophobic tails, and a central moiety between the head group and the one or more tails. The head group can include an amine; for example an amine having a desired pKa. The pKa can be influenced by the structure of the lipid, particularly the nature of head group; e.g., the presence, absence, and location of functional groups such as anionic functional groups, hydrogen bond donor functional groups, hydrogen bond acceptor groups, hydrophobic groups (e.g., aliphatic groups), hydrophilic groups (e.g., hydroxyl or methoxy), or aryl groups. The head group amine can be a cationic amine; a primary, secondary, or tertiary amine; the head group can include one amine group (monoamine), two amine groups (diamine), three amine groups (triamine), or a larger number of amine groups, as in an oligoamine or polyamine. The head group can include a functional group that is less strongly basic than an amine, such as, for example, an imidazole, a pyridine, or a guanidinium group. The head group can be zwitterionic. Other head groups are suitable as well.
Representative central moieties include, but are not limited to, a central carbon atom, a central nitrogen atom, a central carbocyclic group, a central aryl group, a central hetrocyclic group (e.g., central tetrahydrofuranyl group or central pyrrolidinyl group) and a central heteroaryl group. Additionally, the central moiety can include, for example, a glyceride linker, an acyclic glyceride analog linker, or a cyclic linker (including a spiro linker, a bicyclic linker, and a polycyclic linker). The central moiety can include functional groups such as an ether, an ester, a phosphate, a phosphonate, a phosphorothioate, a sulfonate, a disulfide, an acetal, a ketal, an imine, a hydrazone, or an oxime. Other central moieties and functional groups are suitable as well.
In one embodiment, the cationic lipid is a racemic mixture. In another embodiment, the cationic lipid is enriched in one diastereomer, e.g. the cationic lipid has at least 95%, at least 90%, at least 80% or at least 70% diastereomeric excess. In yet another embodiment, the cationic lipid is enriched in one enantiomer, e.g. the lipid has at least 95%, at least 90%, at least 80% or at least 70% enantiomer excess. In yet another embodiment, the cationic lipid is chirally pure, e.g. is a single optical isomer. In yet another embodiment, the cationic lipid is enriched for one optical isomer.
Where a double bond is present (e.g., a carbon-carbon double bond or carbon-nitrogen double bond), there can be isomerism in the configuration about the double bond (i.e. cis/trans or E/Z isomerism). Where the configuration of a double bond is illustrated in a chemical structure, it is understood that the corresponding isomer can also be present. The amount of isomer present can vary, depending on the relative stabilities of the isomers and the energy required to convert between the isomers. Accordingly, some double bonds are, for practical purposes, present in only a single configuration, whereas others (e.g., where the relative stabilities are similar and the energy of conversion low) may be present as inseparable equilibrium mixture of configurations.
In some cases, a double-bonded unsaturation is replaced by a cyclic unsaturation. The cyclic unsaturation can be a cycloaliphatic unsaturation, e.g., a cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, or cyclooctyl group. In some cases, the cyclic group can be a polycyclic group, e.g., a bicyclic group or tricyclic group. A bicyclic group can be bridged, fused, or have a spiro st oiety can be replaced by a cyclopropyl moiety, e.g.,
Figure imgf000040_0001
The cationic lipid includes one or more biodegradable groups. The biodegradable group(s) include one or more bonds that may undergo bond breaking reactions in a biological environment, e.g., in an organism, organ, tissue, cell, or organelle. Functional groups that contain a biodegradable bond include, for example, esters, dithiols, and oximes. Biodegradation can be a factor that influences the clearance of the compound from the body when administered to a subject. Biodegredation can be measured in a cell based assay, where a formulation including a cationic lipid is exposed to cells, and samples are taken at various time points. The lipid fractions can be extracted from the cells and separated and analyzed by LC-MS. From the LC-MS data, rates of biodegradation (e.g., as t values) can be measured.
For example, the compound
Figure imgf000040_0002
(Compound 1) includes an ester linkage in each aliphatic chain, which can undergo hydrolysis in a biological environment, for example, when exposed to, e.g., a lipase or an esterase. The structure of the compound, of course, influences the rate at which the compound undergoes biodegradation. Thus, a compound where the methyl substituent is on the other side of the biodegradable group such as
Figure imgf000041_0001
would be expected to exhibit a different rate of biodegradation. Greater effects on that rate would be expected from changes in the structure of the compound at the site of hydrolysis. One modification that can influence the rate of hydrolysis, and thereby influence the rate of biodegradation and clearance from a subject's body, is to make the leaving group of the hydrolysis reaction have a secondary, rather than primary, alcohol.
For example, without wishing to be bound by theory, Compound 1 shown above may be metabolized as shown in the scheme below:
Figure imgf000041_0002
In one embodiment, a cationic lipid of any of the embodiments described herein has an in vivo half life (t1/2) (e.g., in the liver, spleen or plasma) of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours. The cationic lipid preferably remains intact, or has a half-life sufficient to form a stable lipid nanoparticle which effectively delivers the desired active pharmaceutical ingredient (e.g., a nucleic acid) to its target but thereafter rapidly degrades to minimize any side effects to the subject. For instance, in mice, the cationic lipid preferably has a ti/2 in the spleen of from about 1 to about 7 hours.
In another embodiment, a cationic lipid of any of the embodiments described herein containing a biodegradable group or groups has an in vivo half life (t1/2) (e.g., in the liver, spleen or plasma) of less than about 10% (e.g., less than about 7.5%, less than about 5%, less than about 2.5%) of that for the same cationic lipid without the biodegrable group or groups.
Some cationic lipids can be conveniently represented as a hydrophobic group combined via a central moiety (such as a carbon atom) with a headgroup. By way of example, the compound:
Figure imgf000042_0001
can be thought of as a combination of a headgroup, a central moiety, and two hydrophobic groups as follows:
Figure imgf000042_0002
The present invention includes compounds composed of any combination of the head and hydrophobic groups listed below (in combination with a central moiety (such as a central carbon atom).
Some suitable head groups include those depicted in Table 1A:
Table 1A
Figure imgf000043_0001
Figure imgf000044_0001
Suitable primary groups include, but are not limited to, those that are a combination of a head group from table 1A with a central carbon atom. Other suitable primary groups include those in table IB below: Table IB
Figure imgf000045_0002
Some suitable hydrophobic tail groups include those depicted in Table 1C:
Table 1C
Figure imgf000045_0001
Figure imgf000046_0001
Figure imgf000047_0001
Other suitable tail groups includes those of the formula -R 12 -M 1 -R 13 where R 12 is a C4-
C14 alkyl or C4-C14 alkenyl, M 1 is a biodegradable group as defined above, and R 13 is a branched
12 alkyl or alkenyl (e.g., a Cio-C2o alkyl or Q0-C20 alkenyl), such that (i) the chain length of -R -
M 1 -R 13 is at most 21 atoms (i.e., the total length of the tail from the first carbon after the tertiary carbon (marked with an asterisk) to a terminus of the tail is at most 21), and (ii) the group -R 12 -
M 1 -R 13 has at least 20 carbon atoms (e.g., at least 21 or 22 carbon atoms).
In one preferred embodiment, the chain length of -R 12 -M 1 -R 13 is at most 21 (e.g., at most 20). For example, the chain length can be from about 17 to about 24 or from about 18 to about 20.
In one embodiment, the total carbon atom content of each tail (-R 12 -M 1 -R 13 ) is from about 17 to about 26. For example, the total carbon atom content can be from about 19 to about 26 or from about 21 to about 26.
In one embodiment, the tail has the formula:
Figure imgf000048_0001
where R is an alkyl or alkenyl group having from about 13 to about 17 carbon atoms, and the total carbon length of the tail from the first carbon (the leftmost carbon atom above) to a terminus of the tail is at most 20. Preferably, the tail has from about 22 to about 26 carbon atoms. In one embodiment, the maximum length of R 13 from its attachment point to the ester group of the compound is 12 carbon atoms (e.g., the maximum length can be 11 carbon atoms). In one preferred embodiment, the branch in the alkyl or alkenyl group is at the δ-position or later from the point of attachment of R 13 to the ester group. Suitable R 13 groups include, but are not limited to
Figure imgf000049_0001
Figure imgf000049_0002
C16 (C24) C17 (C25)
Length: C10 (19) Length: C1 1 (20)
Figure imgf000049_0003
C13 (C21 ) C15 (C23)
Length: C8 (17) Length: C9 (18)
For example, the cationic lipid can be
Figure imgf000049_0004
or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), where R is selected from the groups mentioned above.
Another example is a tail of the formula
Figure imgf000050_0001
where R is an alkyl or alkenyl group having from about 13 to about 15 carbon atoms, and the total carbon length of the tail from the first carbon (i.e., the leftmost carbon atom, which is attached to a tertiary carbon) to a terminus of the tail is at most 20. Preferably, the tail has from about 24 to about 26 carbon atoms. In one embodiment, the maximum length of R 13 from its attachment point to the ester group of the compound is 10 carbon atoms (e.g., the maximum length can be 9 carbon atoms). In one preferred embodiment, the branch in the alkyl or alkenyl group is at the δ-position or later from the point of attachment of R 13 to the ester group. Suitable
R 13 groups include, but are not limited to
Figure imgf000050_0002
C13 (C23) C14 (C24)
Length: C9 (20) Length: C9 (20)
Figure imgf000050_0003
C13 (C23) C14 (C24)
Length: C9 (20) Length: C9 (20)
Figure imgf000050_0004
C13 (C24)
Length: C8 (19) For example, the cationic lipid can be
Figure imgf000051_0001
or a salt thereof (e.g., a pharmaceutically acceptable salt thereof), where R is selected from the groups above.
The R group may be derived from a natural product, such as dihydrocitgronellol, lavandulol, phytol, or dihydrophytol. In one embodiment, the R 13 group in the tails above is a dihydrocitronellol group (either as a racemic group or a chirally pure group):
Figure imgf000051_0002
For example, the cationic lipid having a dihydroitronellol group can be
Figure imgf000051_0003
or
Figure imgf000051_0004
or a salt thereof.
In another embodiment, the R group in the tails above is a lavandulol group or a homolog of it as shown below:
Figure imgf000052_0001
Figure imgf000052_0002
Figure imgf000052_0003
Figure imgf000052_0004
A cationic lipid of the fomula:
Figure imgf000052_0005
can also be thought of as a combination of a headgroup, a linker moiety, and two parts of the hydrophobic chains as follows: Head
Figure imgf000053_0001
Biocleavable moiety I
Various headgrops, linker moieties, and hydrophobic chains I and II are listed below. The present invention includes compounds composed of any combination of the head, linker, hydrophobic chain I, and hydrophobic chain II groups listed below.
Table 2A - Representative headgroups
Figure imgf000053_0002
Figure imgf000054_0001
Table 2B - Representative linker groups
Figure imgf000054_0002
Figure imgf000055_0001
Table 2C - Representative hydrophobic chain I and/or la, and combination thereof
Figure imgf000055_0002
p = 0-15, q = 0-15 p = 0-15, q = 1-4, r = 0-15
p = 0-15, q = 1-4, r = 0-15
OMe
p = 0-15, q = 0-6 p = 0-15
R
' m 'n
n = 1-7
m = 0-4; n = 0-4;
R = Me, Et, Pr, iPr, Bu, iBu
R m = 1-4, n = 1-10, p = 0-15, q = 0-15
R = Me, Et, OMe
Table 2D - Representative biodegradable moieties I and/or la and combinations thereof
Figure imgf000056_0001
Figure imgf000057_0001
Table 2E - Representative hydrophobic chain II and/or Ila and combinations thereof
Figure imgf000057_0003
Other cationic lipids of the present invention include those in Table 3 below. Each asymmetric carbon atom in the compounds below can be either chirally pure (R or S) or racemic. These cationic lipids as well as those in the working examples (such as Examples 36 and 37) are suitable for forming nucleic acid-lipid particles.
Figure imgf000057_0002
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000060_0001
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
^— ~—
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Figure imgf000076_0001
Figure imgf000077_0001
Figure imgf000078_0001
In another aspect, the present invention relates to a method of preparing a compound of Formula I-VII. Suitable exemplary synthetic methods are illustrated in Schemes 1-27 shown in the Examples section below.
In one embodiment, the cationic lipid of the present invention is selected from the following compounds, and salts thereof (including pharmaceutically acceptable salts thereof). These cationic lipids are suitable for forming nucleic acid-lipid particles.
Figure imgf000079_0001
Figure imgf000080_0001
-79-
Figure imgf000081_0001
- 80-
Figure imgf000082_0001
In another embodiment, the cationic lipid of the present invention is selected from following compounds, and salts thereof (including pharmaceutically acceptable salts thereof):
Figure imgf000083_0001
Figure imgf000084_0001
Figure imgf000084_0002
Figure imgf000084_0003
Figure imgf000084_0004
Figure imgf000084_0005
Figure imgf000084_0006
Figure imgf000084_0007
Figure imgf000085_0001
In another embodiment, the cationic lipid of the present invention is selected from the following compounds, and salts thereof (including pharmaceutically acceptable salts thereof):
Figure imgf000086_0001
-85-
Figure imgf000087_0001
Additional re resentative cationic lipids include, but are not limited to:
Figure imgf000087_0002
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
Figure imgf000091_0001
-90-
Figure imgf000092_0001
Figure imgf000093_0001
-92-
Figure imgf000094_0001
Figure imgf000095_0001
Figure imgf000096_0001
Figure imgf000097_0001
X = 0, S, NH, CH2
Figure imgf000098_0001
X = O, S, NH, CH2
Figure imgf000098_0002
X = 0, S, NH, CH2 r=0, l,or2
Figure imgf000098_0003
X = 0, S, NR, CH2
r=0 l,or2
Figure imgf000098_0004
r=0 l,or2
Figure imgf000098_0005
Figure imgf000099_0001
m = 0-5 n = 0, 1, or 2
Figure imgf000100_0001
X = O, S, NR, CH2
m = 0-5, n = 0, 1, or 2
Figure imgf000100_0002
n = 0 1, or 2
Figure imgf000100_0003
n = 0, 1, or 2
Figure imgf000100_0004
n = 0 1, or 2
Figure imgf000100_0005
n = 0, 1, or 2
Figure imgf000101_0001
Figure imgf000102_0001
Figure imgf000103_0001
Figure imgf000104_0001
- 103 -
Figure imgf000105_0001
Figure imgf000106_0001
- 105 -
Figure imgf000107_0001
- 106-
Figure imgf000108_0001
Figure imgf000109_0001
Alternatively, for the compounds above having a head of the formula
Figure imgf000109_0002
(where X can be, for example, -C(O)O-), the head can have one methylene unit between the X group (or other functional group) and nitrogen atom. For example, the head can be:
Figure imgf000109_0003
Cationic lipids include those having alternative fatty acid groups and other dialkylamino groups than those shown, including those in which the alkyl substituents are different (e.g., N-ethyl-N-methylamino-, and N-propyl-N-ethylamino-).
In certain embodiments, the cationic lipids have at least one protonatable or deprotonatable group, such that the lipid is positively charged at a pH at or below physiological pH (e.g. pH 7.4), and neutral at a second pH, preferably at or above physiological pH. Such lipids are also referred to as cationic lipids. It will, of course, be understood that the addition or removal of protons as a function of pH is an equilibrium process, and that the reference to a charged or a neutral lipid refers to the nature of the predominant species and does not require that all of the lipid be present in the charged or neutral form. The lipids can have more than one protonatable or deprotonatable group, or can be zwiterrionic.
In certain embodiments, protonatable lipids (i.e., cationic lipids) have a pKa of the protonatable group in the range of about 4 to about 11. For example, the lipids can have a pKa of about 4 to about 7, e.g., from about 5 to about 7, such as from about 5.5 to about 6.8, when incorporated into lipid particles. Such lipids may be cationic at a lower pH formulation stage, while particles will be largely (though not completely) surface neutralized at physiological pH around pH 7.4.
In particular embodiments, the lipids are charged lipids. As used herein, the term "charged lipid" includes, but is not limited to, those lipids having one or two fatty acyl or fatty alkyl chains and a quaternary amino head group. The quaternary amine carries a permanent positive charge. The head group can optionally include an ionizable group, such as a primary, secondary, or tertiary amine that may be protonated at physiological pH. The presence of the quaternary amine can alter the pKa of the ionizable group relative to the pKa of the group in a structurally similar compound that lacks the quaternary amine (e.g., the quaternary amine is replaced by a tertiary amine).
Included in the instant invention is the free form of the cationic lipids described herein, as well as pharmaceutically acceptable salts and stereoisomers thereof. The cationic lipid can be a protonated salt of the amine cationic lipid. The term "free form" refers to the amine cationic lipids in non-salt form. The free form may be regenerated by treating the salt with a suitable dilute aqueous base solution such as dilute aqueous NaOH, potassium carbonate, ammonia and sodium bicarbonate.
The pharmaceutically acceptable salts of the instant cationic lipids can be synthesized from the cationic lipids of this invention which contain a basic or acidic moiety by conventional chemical methods. Generally, the salts of the basic cationic lipids are prepared either by ion exchange chromatography or by reacting the free base with stoichiometric amounts or with an excess of the desired salt-forming inorganic or organic acid in a suitable solvent or various combinations of solvents. Similarly, the salts of the acidic compounds are formed by reactions with the appropriate inorganic or organic base.
Thus, pharmaceutically acceptable salts of the cationic lipids of this invention include non-toxic salts of the cationic lipids of this invention as formed by reacting a basic instant cationic lipids with an inorganic or organic acid. For example, non-toxic salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like, as well as salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, sulfanilic, 2-acetoxy-benzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, and trifluoroacetic (TFA).
When the cationic lipids of the present invention are acidic, suitable "pharmaceutically acceptable salts" refers to salts prepared form pharmaceutically acceptable non-toxic bases including inorganic bases and organic bases. Salts derived from inorganic bases include aluminum, ammonium, calcium, copper, ferric, ferrous, lithium, magnesium, manganic salts, manganous, potassium, sodium, and zinc. In one embodiment, the base is selected from ammonium, calcium, magnesium, potassium and sodium. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as arginine, betaine caffeine, choline, N^-dibenzylethylenediamine, diethylamin, 2-diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine, ethylenediamine, N-ethylmorpholine, N-ethylpiperidine, glucamine, glucosamine, histidine, hydrabamine, isopropylamine, lysine, methylglucamine, morpholine, piperazine, piperidine, polyamine resins, procaine, purines, theobromine, triethylamine, trimethylamine tripropylamine, and tromethamine.
It will also be noted that the cationic lipids of the present invention may potentially be internal salts or zwitterions, since under physiological conditions a deprotonated acidic moiety in the compound, such as a carboxyl group, may be anionic, and this electronic charge might then be balanced off internally against the cationic charge of a protonated or alkylated basic moiety, such as a quaternary nitrogen atom. One or more additional cationic lipids, which carry a net positive charge at about physiological pH, in addition to those specifically described above, may also be included in the lipid particles and compositions described herein. Such cationic lipids include, but are not limited to N,N-dioleyl-N,N-dimethylammonium chloride ("DODAC")
N-(2,3-dioleyloxy)propyl-N,N-N-triethylammonium chloride ("DOTMA")
N,N-distearyl-N,N-dimethylammonium bromide ("DDAB")
N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride ("DOTAP") l,2-Dioleyloxy-3-trimethylaminopropane chloride salt ("DOTAP. CI")
3P-(N-(N',N'-dimethylaminoethane)-carbamoyl)cholesterol ("DC-Choi"), N-(l-(2,3-dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate ("DOSPA"), dioctadecylamidoglycyl carboxyspermine ("DOGS"), l,2-dileoyl-sn-3-phosphoethanolamine ("DOPE"), l,2-dioleoyl-3-dimethylammonium propane ("DODAP"), N, N-dimethyl-2,3-dioleyloxy)propylamine ("DODMA"), and N-(l,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammonium bromide ("DMRIE"). Additionally, a number of commercial preparations of cationic lipids can be used, such as, e.g. , LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), and LIPOFECT AMINE (comprising DOSPA and DOPE, available from GIBCO/BRL).
PEG Lipids
Suitable head groups for the PEG lipids include, but are not limited to those shown in Table 3 below.
Table 3
Figure imgf000112_0001
- I l l -
Figure imgf000113_0001
wherein
n is an integer from 10 to 100 (e.g. 20-50 or 40-50);
s, s', t and t' are independently 0, 1, 2, 3, 4, 5, 6 or 7; and m is 1, 2, 3, 4, 5, or 6. Other representative PEG lipids include, but are not limited to: r = 20-45
X = Y = CH2, O, S
Figure imgf000115_0001
X = Y = CH2,0,S m = 0_3
Figure imgf000115_0002
0-10
Figure imgf000116_0001
- 115 - R = alkyl, substituted alkyl, aryl, benzyl
The Other Lipid Components
The lipid particles and compositions described herein may also include one or more neutral lipids. Neutral lipids, when present, can be any of a number of lipid species which exist either in an uncharged or neutral zwitterionic form at physiological pH. Such lipids include, for example, diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, dihydrosphingomyelin, cephalin, and cerebrosides. In one embodiment, the neutral lipid component is a lipid having two acyl groups (e.g., diacylphosphatidylcholine and diacylphosphatidylethanolamine). In one embodiment, the neutral lipid contains saturated fatty acids with carbon chain lengths in the range of C10 to C2o- In another embodiment, the neutral lipid includes mono or diunsaturated fatty acids with carbon chain lengths in the range of C10 to C20. Suitable neutral lipids include, but are not limited to, DSPC, DPPC, POPC, DOPE, DSPC, and SM.
The lipid particles and compositions described herein may also include one or more lipids capable of reducing aggregation. Examples of lipids that reduce aggregation of particles during formation include polyethylene glycol (PEG)-modified lipids (PEG lipids, such as PEG-DMG and PEG-DMA), monosialoganglioside Gml, and polyamide oligomers ("PAO") such as (described in U.S. Patent No. 6,320,017, which is incorporated by reference in its entirety). Suitable PEG lipids include, but are not limited to, PEG-modified phosphatidylethanolamine and phosphatidic acid, PEG-ceramide conjugates (e.g., PEG-CerC14 or PEG-CerC20) (such as those described in U.S. Patent No. 5,820,873, incorporated herein by reference), PEG-modified dialkylamines and PEG-modified l,2-diacyloxypropan-3-amines, PEG-modified diacylglycerols and dialkylglycerols, mPEG (mw2000)-diastearoylphosphatidylethanolamine (PEG-DSPE). The lipid particles and compositions may include a sterol, such as cholesterol.
Lipid Particles
In a further aspect, the present invent relates to lipid particles that include one or more of the cationic lipids described herein. In one embodiment, the lipid particle includes one or more compounds of formula I- VII.
Lipid particles include, but are not limited to, liposomes. As used herein, a liposome is a structure having lipid-containing membranes enclosing an aqueous interior.
Another embodiment is a nucleic acid- lipid particle (e.g., a SNALP) comprising a cationic lipid of the present invention, a non-cationic lipid (such as a neutral lipid), optionally a PEG-lipid conjugate (such as the lipids for reducing aggregation of lipid particles discussed herein), optionally a sterol (e.g., cholesterol), and a nucleic acid. As used herein, the term "SNALP" refers to a stable nucleic acid-lipid particle. A SNALP represents a particle made from lipids, wherein the nucleic acid (e.g., an interfering RNA) is encapsulated within the lipids. In certain instances, SNALPs are useful for systemic applications, as they can exhibit extended circulation lifetimes following intravenous (i.v.) injection, they can accumulate at distal sites (e.g., sites physically separated from the administration site), and they can mediate silencing of target gene expression at these distal sites. The nucleic acid may be complexed with a condensing agent and encapsulated within a SNALP as set forth in International Publication No. WO 00/03683, the disclosure of which is herein incorporated by reference in its entirety.
For example, the lipid particle may include a cationic lipid, a fusion-promoting lipid (e.g., DPPC), a neutral lipid, cholesterol, and a PEG-modified lipid. In one embodiment, the lipid particle includes the above lipid mixture in molar ratios of about 20-70% cationic lipid: 0.1-50% fusion promoting lipid: 5-45% neutral lipid: 20-55% cholesterol: 0.5-15% PEG-modified lipid (based upon 100% total moles of lipid in the lipid particle).
In another embodiment of the lipid particle, the cationic lipid is present in a mole percentage of about 20% and about 60%; the neutral lipid is present in a mole percentage of about 5% to about 25%; the sterol is present in a mole percentage of about 25% to about 55%; and the PEG lipid is PEG-DMA, PEG-DMG, or a combination thereof, and is present in a mole percentage of about 0.5% to about 15% (based upon 100% total moles of lipid in the lipid particle).
In particular embodiments, the molar lipid ratio, with regard to mol% cationic lipid/DSPC/Chol/PEG-DMG or PEG-DMA) is approximately 40/10/40/10, 35/15/40/10 or 52/13/30/5. This mixture may be further combined with a fusion-promoting lipid in a molar ratio of 0.1-50%, 0.1-50%, 0.5-50%, 1-50%, 5%-45%, 10%-40%, or 15%-35%. In other words, when a 40/10/40/10 mixture of lipid/DSPC/Chol/PEG-DMG or PEG-DMA is combined with a fusion- promoting peptide in a molar ratio of 50%, the resulting lipid particles can have a total molar ratio of (mol% cationic lipid/DSPC/Chol/PEG-DMG or PEG-DMA/fusion-promoting peptide) 20/5/20/5/50. In another embodiment, the neutral lipid, DSPC, in these compositions is replaced with POPC, DPPC, DOPE or SM.
In one embodiment, the lipid particles comprise a cationic lipid of the present invention, a neutral lipid, a sterol and a PEG-modified lipid. In one embodiment, the lipid particles include from about 25% to about 75% on a molar basis of cationic lipid, e.g., from about 35 to about 65%, from about 45 to about 65%, about 60%, about 57.5%, about 57.1%, about 50% or about 40% on a molar basis. In one embodiment, the lipid particles include from about 0% to about 15% on a molar basis of the neutral lipid, e.g., from about 3 to about 12%, from about 5 to about 10%, about 15%, about 10%, about 7.5%, about 7.1% or about 0% on a molar basis. In one embodiment, the neutral lipid is DPPC. In one embodiment, the neutral lipid is DSPC. In one embodiment, the formulation includes from about 5% to about 50% on a molar basis of the sterol, e.g., about 15 to about 45%, about 20 to about 40%, about 48%, about 40%, about 38.5%, about 35%, about 34.4%, about 31.5% or about 31% on a molar basis. In one embodiment, the sterol is cholesterol.
The lipid particles described herein may further include one or more therapeutic agents. In a preferred embodiment, the lipid particles include a nucleic acid (e.g., an oligonucleotide), such as siRNA or miRNA. In one embodiment, the lipid particles include from about 0.1% to about 20% on a molar basis of the PEG-modified lipid, e.g., about 0.5 to about 10%, about 0.5 to about 5%, about 10%, about 5%, about 3.5%, about 1.5%, about 0.5%, or about 0.3% on a molar basis. In one embodiment, the PEG-modified lipid is PEG- DMG. In one embodiment, the PEG-modified lipid is PEG-c-DMA. In one embodiment, the lipid particles include 25-75% of cationic lipid, 0.5-15% of the neutral lipid, 5-50% of the sterol, and 0.5- 20% of the PEG-modified lipid on a molar basis.
In one embodiment, the lipid particles include 35-65% of cationic lipid, 3-12% of the neutral lipid, 15-45% of the sterol, and 0.5- 10% of the PEG-modified lipid on a molar basis. In one embodiment, the lipid particles include 45-65% of cationic lipid, 5-10% of the neutral lipid, 25-40% of the sterol, and 0.5- 5% of the PEG-modified lipid on a molar basis. In one embodiment, the PEG modified lipid comprises a PEG molecule of an average molecular weight of 2,000 Da. In one embodiment, the PEG modified lipid is PEG-distyryl glycerol (PEG-DSG).
In one embodiment, the ratio of lipid: siRNA is at least about 0.5: 1, at least about 1: 1, at least about 2: 1, at least about 3: 1, at least about 4: 1, at least about 5: 1, at least about 6: 1, at least about 7: 1, at least about 11: 1 or at least about 33: 1. In one embodiment, the ratio of lipid: siRNA ratio is between about 1: 1 to about 35: 1, about 3: 1 to about 15: 1, about 4: 1 to about 15: 1, or about 5: 1 to about 13: 1. In one embodiment, the ratio of lipid: siRNA ratio is between about 0.5: 1 to about 12: 1.
In one embodiment, the lipid particles are nanoparticles. In additional embodiments, the lipid particles have a mean diameter size of from about 50 nm to about 300 nm, such as from about 50 nm to about 250 nm, for example, from about 50 nm to about 200 nm.
In one embodiment, a lipid particle containing a cationic lipid of any of the embodiments described herein has an in vivo half life (t^) (e.g., in the liver, spleen or plasma) of less than about 3 hours, such as less than about 2.5 hours, less than about 2 hours, less than about 1.5 hours, less than about 1 hour, less than about 0.5 hour or less than about 0.25 hours.
In another embodiment, a lipid particle containing a cationic lipid of any of the embodiments described herein has an in vivo half life (t^) (e.g., in the liver, spleen or plasma) of less than about 10 % (e.g., less than about 7.5%, less than about 5%, less than about 2.5%) of that for the same cationic lipid without the biodegrable group or groups.
Additional Components
The lipid particles and compositions described herein can further include one or more antioxidants. The antioxidant stabilizes the lipid particle and prevents, decreases, and/or inhibits degradation of the cationic lipid and/or active agent present in the lipid particles. The antioxidant can be a hydrophilic antioxidant, a lipophilic antioxidant, a metal chelator, a primary antioxidant, a secondary antioxidant, salts thereof, and mixtures thereof. In certain embodiments, the antioxidant comprises a metal chelator such as EDTA or salts thereof, alone or in combination with one, two, three, four, five, six, seven, eight, or more additional antioxidants such as primary antioxidants, secondary antioxidants, or other metal chelators. In one preferred embodiment, the antioxidant comprises a metal chelator such as EDTA or salts thereof in a mixture with one or more primary antioxidants and/or secondary antioxidants. For example, the antioxidant may comprise a mixture of EDTA or a salt thereof, a primary antioxidant such as a- tocopherol or a salt thereof, and a secondary antioxidant such as ascorbyl palmitate or a salt thereof. In one embodiment, the antioxidant comprises at least about 100 mM citrate or a salt thereof. Examples of antioxidants include, but are not limited to, hydrophilic antioxidants, lipophilic antioxidants, and mixtures thereof. Non-limiting examples of hydrophilic antioxidants include chelating agents (e.g., metal chelators) such as ethylenediaminetetraacetic acid (EDTA), citrate, ethylene glycol tetraacetic acid (EGTA), l,2-bis(o-aminophenoxy)ethane-N,N,N',N'- tetraacetic acid (BAPTA), diethylene triamine pentaacetic acid (DTPA), 2,3-dimercapto-l- propanesulfonic acid (DMPS), dimercap to succinic acid (DMSA), cc-lipoic acid, salicylaldehyde isonicotinoyl hydrazone (SIH), hexyl thioethylamine hydrochloride (HTA), desferrioxamine, salts thereof, and mixtures thereof. Additional hydrophilic antioxidants include ascorbic acid, cysteine, glutathione, dihydrolipoic acid, 2- mercaptoethane sulfonic acid, 2- mercaptobenzimidazole sulfonic acid, 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid, sodium metabisulfite, salts thereof, and mixtures thereof. Non-limiting examples of lipophilic antioxidants include vitamin E isomers such as α-, β-, γ-, and δ-tocopherols and α-, β-, γ-, and δ- tocotrienols; polyphenols such as 2-tert-butyl-4-methyl phenol, 2-fert-butyl-5-methyl phenol, and 2-tert-butyl-6-methyl phenol; butylated hydroxyanisole (BHA) (e.g., 2-teri-butyl-4- hydroxyanisole and 3-tert-butyl-4-hydroxyanisole); butylhydroxytoluene (BHT); tert- butylhydroquinone (TBHQ); ascorbyl palmitate; rc-propyl gallate; salts thereof; and mixtures thereof. Suitable antioxidants and formulations containing such antioxidants are described in International Publication No. WO 2011/066651, which is hereby incorporated by reference.
In another embodiment, the lipid particles or compositions contain the antioxidant EDTA (or a salt thereof), the antioxidant citrate (or a salt thereof), or EDTA (or a salt thereof) in combination with one or more (e.g., a mixture of) primary and/or secondary antioxidants such as a- tocopherol (or a salt thereof) and/or ascorbyl palmitate (or a salt thereof).
In one embodiment, the antioxidant is present in an amount sufficient to prevent, inhibit, or reduce the degradation of the cationic lipid present in the lipid particle. For example, the antioxidant may be present at a concentration of at least about or about 0.1 mM, 0.5 mM, 1 mM, 10 mM, 100 mM, 500 mM, 1 M, 2 M, or 5M, or from about 0.1 mM to about 1 M, from about 0.1 mM to about 500 mM, from about 0.1 mM to about 250 mM, or from about 0.1 mM to about 100 mM.
The lipid particles and compositions described herein can further include an apolipoprotein. As used herein, the term "apolipoprotein" or "lipoprotein" refers to apolipoproteins known to those of skill in the art and variants and fragments thereof and to apolipoprotein agonists, analogues or fragments thereof described below.
In a preferred embodiment, the active agent is a nucleic acid, such as a siRNA. For example, the active agent can be a nucleic acid encoded with a product of interest, including but not limited to, RNA, antisense oligonucleotide, an antagomir, a DNA, a plasmid, a ribosomal RNA (rRNA), a micro RNA (miRNA) (e.g., a miRNA which is single stranded and 17-25 nucleotides in length), transfer RNA (tRNA), a small interfering RNA (siRNA), small nuclear RNA (snRNA), antigens, fragments thereof, proteins, peptides, vaccines and small molecules or mixtures thereof. In one more preferred embodiment, the nucleic acid is an oligonucleotide (e.g., 15-50 nucleotides in length (or 15-30 or 20-30 nucleotides in length)). An siRNA can have, for instance, a duplex region that is 16-30 nucleotides long. In another embodiment, the nucleic acid is an immuno stimulatory oligonucleotide, decoy oligonucleotide, supermir, miRNA mimic, or miRNA inhibitor. A supermir refers to a single stranded, double stranded or partially double stranded oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or both or modifications thereof, which has a nucleotide sequence that is substantially identical to an miRNA and that is antisense with respect to its target. miRNA mimics represent a class of molecules that can be used to imitate the gene silencing ability of one or more miRNAs. Thus, the term "microRNA mimic" refers to synthetic non-coding RNAs (i.e. the miRNA is not obtained by purification from a source of the endogenous miRNA) that are capable of entering the RNAi pathway and regulating gene expression.
The nucleic acid that is present in a lipid-nucleic acid particle can be in any form. The nucleic acid can, for example, be single-stranded DNA or RNA, or double- stranded DNA or RNA, or DNA-RNA hybrids. Non-limiting examples of double- stranded RNA include siRNA. Single- stranded nucleic acids include, e.g. , antisense oligonucleotides, ribozymes, microRNA, and triplex-forming oligonucleotides. The lipid particles of the present invention can also deliver nucleic acids which are conjugated to one or more ligands.
Pharmaceutical Compositions
The lipid particles, particularly when associated with a therapeutic agent, may be formulated as a pharmaceutical composition, e.g., which further comprises a pharmaceutically acceptable diluent, excipient, or carrier, such as physiological saline or phosphate buffer.
The resulting pharmaceutical preparations may be sterilized by conventional, well known sterilization techniques. The aqueous solutions can then be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, and tonicity adjusting agents, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, and calcium chloride. Additionally, the lipidic suspension may include lipid-protective agents which protect lipids against free -radical and lipid-peroxidative damages on storage. Lipophilic free-radical quenchers, such as a-tocopherol and water-soluble iron-specific chelators, such as ferrioxamine, are suitable.
The concentration of lipid particle or lipid-nucleic acid particle in the pharmaceutical formulations can vary, for example, from less than about 0.01%, to at or at least about 0.05-5% to as much as 10 to 30% by weight.
Methods of Manufacture
Methods of making cationic lipids, lipid particles containing them, and pharmaceutical compositions containing the cationic lipids and/or lipid particles are described in, for example, International Publication Nos. WO 2010/054406, WO 2010/054401, WO 2010/054405, WO 2010/054384, WO 2010/042877, WO 2010/129709, WO 2009/086558, and WO 2008/042973, and U.S. Patent Publication Nos. 2004/0142025, 2006/0051405 and 2007/0042031, each of which is incorporated by reference in its entirety.
For example, in one embodiment, a solution of one or more lipids (including a cationic lipid of any of the embodiments described herein) in an organic solution (e.g., ethanol) is prepared. Similarly, a solution of one or more active (therapeutic) agents (such as, for example an siRNA molecule or a 1: 1 molar mixture of two siRNA molecules) in an aqueous buffered (e.g., citrate buffer) solution is prepared. The two solutions are mixed and diluted to form a colloidal suspension of siRNA lipid particles. In one embodiment, the siRNA lipid particles have an average particle size of about 80-90 nm. In further embodiments, the dispersion may be filtered through 0.45/2 micron filters, concentrated and diafiltered by tangential flow filtration.
Definitions
As used herein, the term "cationic lipid" inlcudes those lipids having one or two fatty acid or fatty aliphatic chains and an amino acid containing head group that may be protonated to form a cationic lipid at physiological pH. In some embodiments, a cationic lipid is referred to as an "amino acid conjugate cationic lipid."
A subject or patient in whom administration of the complex is an effective therapeutic regimen for a disease or disorder is preferably a human, but can be any animal, including a laboratory animal in the context of a clinical trial or screening or activity experiment. Thus, as can be readily appreciated by one of ordinary skill in the art, the methods, compounds and compositions of the present invention are particularly suited to administration to any animal, particularly a mammal, and including, but by no means limited to, humans, domestic animals, such as feline or canine subjects, farm animals, such as but not limited to bovine, equine, caprine, ovine, and porcine subjects, wild animals (whether in the wild or in a zoological garden), research animals, such as mice, rats, rabbits, goats, sheep, pigs, dogs, and cats, avian species, such as chickens, turkeys, and songbirds, i.e., for veterinary medical use.
Many of the chemical groups recited in the generic formulas above are written in a particular order (for example, -OC(O)-). It is intended that the chemical group is to be incorporated into the generic formula in the order presented unless indicated otherwise. For example, a generic formula of the form -(R)i-(M1)k-(R)m- where M1 is -C(0)0- and k is 1 refers to -(R)i-C(0)0-(R)m- unless specified otherwise. It is to be understood that when a chemical group is written in a particular order, the reverse order is also contemplated unless otherwise specified. For example, in a generic formula -(R)i-(M1)k-(R)m- where M1 is defined as - C(0)NH- (i.e., -(R)i-C(0)-NH-(R)m-), the compound where M1 is -NHC(O)- (i.e., -(R);- NHC(0)-(R)m-) is also contemplated unless otherwise specified.
The term "biodegradable cationic lipid" refers to a cationic lipid having one or more biodegradable groups located in the mid- or distal section of a lipidic moiety (e.g., a hydrophobic chain) of the cationic lipid. The incorporation of the biodegradable group(s) into the cationic lipid results in faster metabolism and removal of the cationic lipid from the body following delivery of the active pharmaceutical ingredient to a target area.
As used herein, the term "biodegradable group" refers to a group that include one or more bonds that may undergo bond breaking reactions in a biological environment, e.g., in an organism, organ, tissue, cell, or organelle. For example, the biodegradable group may be metabolizable by the body of a mammal, such as a human (e.g., by hydrolysis). Some groups that contain a biodegradable bond include, for example, but are not limited to esters, dithiols, and oximes. Non-limiting examples of biodegradable groups are -OC(O)-, -C(0)0-, -SC(O)-, - C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, - C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - OSi(R5)20-, -C(0)(CR3R4)C(0)0-, or -OC(0)(CR3R4)C(0)-.
As used herein, an "aliphatic" group is a non-aromatic group in which carbon atoms are linked into chains, and is either saturated or unsaturated.
The terms "alkyl" and "alkylene" refer to a straight or branched chain saturated hydrocarbon moiety. In one embodiment, the alkyl group is a straight chain saturated hydrocarbon. Unless otherwise specified, the "alkyl" or "alkylene" group contains from 1 to 24 carbon atoms. Representative saturated straight chain alkyl groups include methyl, ethyl, n-propyl, n-butyl, n-pentyl, and n-hexyl. Representative saturated branched alkyl groups include isopropyl, sec-butyl, isobutyl, ie/t-butyl, and isopentyl.
The term "alkenyl" refers to a straight or branched chain hydrocarbon moiety having one or more carbon-carbon double bonds. In one embodiment, the alkenyl group contains 1, 2, or 3 double bonds and is otherwise saturated. Unless otherwise specified, the "alkenyl" group contains from 2 to 24 carbon atoms. Alkenyl groups include both cis and trans isomers. Representative straight chain and branched alkenyl groups include ethylenyl, propylenyl,
1- butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl, 3-methyl-l-butenyl,
2- methyl-2-butenyl, and 2,3-dimethyl-2-butenyl.
The term "alkynyl" refers to a straight or branched chain hydrocarbon moiety having one or more carbon-carbon triple bonds. Unless otherwise specified, the "alkynyl" group contains from 2 to 24 carbon atoms. Representative straight chain and branched alkynyl groups include acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, and 3-methyl-l-butynyl.
Unless otherwise specified, the terms "branched alkyl", "branched alkenyl", and "branched alkynyl" refer to an alkyl, alkenyl, or alkynyl group in which one carbon atom in the group (1) is bound to at least three other carbon atoms and (2) is not a ring atom of a cyclic group. For example, a spirocyclic group in an alkyl, alkenyl, or alkynyl group is not considered a point of branching.
Unless otherwise specified, the term "acyl" refers to a carbonyl group substituted with hydrogen, alkyl, partially saturated or fully saturated cycloalkyl, partially saturated or fully saturated heterocycle, aryl, or heteroaryl. For example, acyl groups include groups such as (C1-C2o)alkanoyl (e.g., formyl, acetyl, propionyl, butyryl, valeryl, caproyl, and t-butylacetyl), (C3-C2o)cycloalkylcarbonyl (e.g., cyclopropylcarbonyl, cyclobutylcarbonyl, cyclopentylcarbonyl, and cyclohexylcarbonyl), heterocyclic carbonyl (e.g., pyrrolidinylcarbonyl, pyrrolid-2-one-5-carbonyl, piperidinylcarbonyl, piperazinylcarbonyl, and tetrahydrofuranylcarbonyl), aroyl (e.g., benzoyl) and heteroaroyl (e.g., thiophenyl-2-carbonyl, thiophenyl-3-carbonyl, furanyl-2-carbonyl, furanyl-3-carbonyl, lH-pyrroyl-2-carbonyl, lH-pyrroyl-3-carbonyl, and benzo[b]thiophenyl-2-carbonyl).
The term "aryl" refers to an aromatic monocyclic, bicyclic, or tricyclic hydrocarbon ring system. Unless otherwise specified, the "aryl" group contains from 6 to 14 carbon atoms. Examples of aryl moieties include, but are not limited to, phenyl, naphthyl, anthracenyl, and pyrenyl.
The terms "cycloalkyl" and "cycloalkylene" refer to a saturated monocyclic or bicyclic hydrocarbon moiety such as cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Unless otherwise specified, the "cycloalkyl" or "cycloalkylene" group contains from 3 to 10 carbon atoms.
The term "cycloalkylalkyl" refers to a cycloalkyl group bound to an alkyl group, where the alkyl group is bound to the rest of the molecule.
The term "heterocycle" (or "heterocyclyl") refers to a non-aromatic 5- to 8-membered monocyclic, or 7- to 12-membered bicyclic, or 11- to 14-membered tricyclic ring system which is either saturated or unsaturated, and which contains from 1 to 3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, independently selected from nitrogen, oxygen and sulfur, and wherein the nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen heteroatom may be optionally quaternized. For instance, the heterocycle may be a cycloalkoxy group. The heterocycle may be attached to the rest of the molecule via any heteroatom or carbon atom in the heterocycle. Heterocycles include, but are not limited to, morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, piperizynyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydroprimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, and tetrahydrothiopyranyl.
The term "heteroaryl" refers to an aromatic 5-8 membered monocyclic, 7-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, where the heteroatoms are selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S if monocyclic, bicyclic, or tricyclic, respectively). The heteroaryl groups herein described may also contain fused rings that share a common carbon-carbon bond.
The term "substituted", unless otherwise indicated, refers to the replacement of one or more hydrogen radicals in a given structure with the radical of a specified substituent including, but not limited to: halo, alkyl, alkenyl, alkynyl, aryl, heterocyclyl, thiol, alkylthio, oxo, thioxy, arylthio, alkylthioalkyl, arylthioalkyl, alkylsulfonyl, alkylsulfonylalkyl, arylsulfonylalkyl, alkoxy, aryloxy, aralkoxy, aminocarbonyl, alkylaminocarbonyl, arylaminocarbonyl, alkoxycarbonyl, aryloxycarbonyl, haloalkyl, amino, trifluoromethyl, cyano, nitro, alkylamino, arylamino, alkylaminoalkyl, arylaminoalkyl, aminoalkylamino, hydroxy, alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, aminocarbonylalkyl, acyl, aralkoxycarbonyl, carboxylic acid, sulfonic acid, sulfonyl, phosphonic acid, aryl, heteroaryl, heterocyclic, and an aliphatic group. It is understood that the substituent may be further substituted. Exemplary substituents include amino, alkylamino, dialkylamino, and cyclic amino compounds.
The term "halogen" or "halo" refers to fluoro, chloro, bromo and iodo.
The following abbreviations may be used in this application:
DSPC: distearoylphosphatidylcholine; DPPC: l,2-Dipalmitoyl-sn-glycero-3-phosphocholine; POPC: 1- palmitoyl-2-oleoyl-sn-phosphatidylcholine; DOPE: l,2-dileoyl-sn-3- phosphoethanolamine; PEG-DMG generally refers to 1,2-dimyristoyl-sn-glycerol-methoxy polyethylene glycol (e.g., PEG 2000); TBDPSC1: tert-Butylchlorodiphenylsilane; DMAP:
dimethylaminopyridine; HMPA: hexamethylphosphoramide; EDC: l-ethyl-3-(3- dimethylaminopropyl) carbodiimide; DIPEA: diisopropylethylamine; DCM: dichloromethane; TEA: triethylamine; TBAF: tetrabutylammonium fluoride
Methods to prepare various organic groups and protective groups are known in the art and their use and modification is generally within the ability of one of skill in the art (see, for example, Green, T.W. et. ah, Protective Groups in Organic Synthesis (1999); Stanley R. Sandler and Wolf Karo, Organic Functional Group Preparations (1989); Greg T. Hermanson,
Bioconjugate Techniques (1996); and Leroy G. Wade, Compendium Of Organic Synthetic Methods (1980)). Briefly, protecting groups are any group that reduces or eliminates unwanted reactivity of a functional group. A protecting group can be added to a functional group to mask its reactivity during certain reactions and then removed to reveal the original functional group. In some embodiments an "alcohol protecting group" is used. An "alcohol protecting group" is any group which decreases or eliminates unwanted reactivity of an alcohol functional group.
Protecting groups can be added and removed using techniques well known in the art.
The compounds may be prepared by at least one of the techniques described herein or known organic synthesis techniques.
Examples
Example 1:
Scheme 1. ALNY-322/quaternary salts
Figure imgf000130_0001
Compound 2: To a solution of compound 1 (10.0 g, 18.8 mmol, see International Publication No. WO 2010/054406) in CH2C12 (80 mL) were added triethylamine (7.86 mL, 56.4 mmol), DMAP (459 mg, 3.76 mmol) and ie/t-butyl(chloro)diphenylsilane (9.62 mL, 37.6 mmol). The reaction mixture was stirred for 24 hours. The mixture was then diluted with CH2C12 and washed with aqueous saturated NaHC03 solution. The organic layer was separated and dried over anhydrous Na2S04. After filtration and concentration, the crude product was purified by silica gel column chromatography (0-5% EtOAc in hexane) to afford 2 (12.4 g, 16.1 mmol, 86%, Rf = 0.24 with hexane). 1H NMR (400 MHz, CDC13) δ 7.66-7.68 (m, 4 H), 7.33-7.42 (m, 6 H), 5.30-5.39 (m, 4 H), 3.67-3.72 (m, 1 H), 1.97-2.04 (m, 8 H), 1.07- 1.42 (m, 52 H), 1.05 (s, 9 H), 0.88 (t, J = 6.8 Hz, 6 H).
Compound 3: To a solution of 2 (12.4 g, 16.1 mmol) in iert-butanol (100 mL), THF (30 mL) and H20 (10 mL) were added 4-methylmorpholine N-oxide (4.15 g, 35.4 mmol) and osmium tetroxide (41 mg, 0.161 mg). The reaction mixture was stirred for 16 hours, then quenched by adding sodium bisulfite. After removing the solvents by evaporation, the residue was extracted with Et20 (500 mL) and H20 (300 mL). The organic layer was separated and dried over anhydrous Na2S04. After filtration and concentration, the crude was purified by silica gel column chromatography (hexane:EtOAc = 1 : 1, Rf = 0.49) to afford 3 (12.7 g, 15.1 mmol, 94%). 1H NMR (400 MHz, CDC13) δ 7.66-7.68 (m, 4 H), 7.33-7.43 (m, 6 H), 3.67-3.73 (m, 1 H), 3.57- 3.62 (m, 4 H), 1.82 (t, J = 5.0 Hz, 4 H), 1.10- 1.51 (m, 60 H), 1.04 (s, 9 H), 0.88 (t, J = 6.8 Hz, 6 H).
Compound 4: To a solution of 3 (12.6 g, 15.0 mmol) in 1,4-dioxane (220 mL), CH2C12 (70 mL), MeOH (55 mL), and H20 (55 mL) was added NaI04 (7.70 g, 36.0 mmol). The reaction mixture was stirred for 16 hours at room temperature. The mixture was extracted with Et20 (500 mL) and H20 (300 mL). The organic layer was separated and dried over anhydrous Na2S04. After filtration and concentration, the crude product was purified by silica gel column chromatography (Hexane:EtOAc = 9: 1, Rf = 0.30) to afford 4 (7.98 g, 14.5 mmol, 97%). Molecular weight for C35H54Na03Si (M+Na)+ Calc. 573.3740, Found 573.3.
Compound 7: To a solution of 5 (see, Tetrahedron, 63, 1140-1145, 2006; 1.09 g, 2.18 mmol) in THF (20 mL) and HMPA (4 mL), LiHMDS (1 M THF solution, 4.36 mL, 4.36 mmol) was added at -20 °C. The resulting mixture was stirred for 20 minutes at the same temperature, then cooled to -78 °C. A solution of 4 (500 mg, 0.908 mmol) in THF (4 mL) was added. The mixture was stirred and allowed to warm to room temperature overnight. MS analysis showed the formation of the di-acid (6; C5 H8505Si (M-H)~ calc. 829.6166, observed 829.5). To the mixture, NaHC03 (1.10 g, 13.1 mmol) and dimethyl sulfate (1.24 mL, 13.1 mmol) were added and stirred for 2 hours at room temperature. The reaction was quenched by adding saturated NH4C1 aqueous solution (50 mL) then extracted with Et20 (2 x 100 mL). The organic layer was separated and dried over anhydrous Na2S04. After filtration and concentration, the crude product was purified by silica gel column chromatography (Hexane:EtOAc = 9: 1, Rf = 0.35) to afford 7 (270 mg, 0.314 mmol, 35%). Molecular weight for CssHgoNaOsSi (M+Na)+ Calc. 881.6455, Found 881.6484.
Compound 8: To a solution of 7 (265 mg, 0.308 mmol) in THF (2.5 mL), w-TBAF (1 M THF solution, 0.555 mL, 0.555 mmol) was added. The reaction mixture was stirred for 14 hours at 45 °C. After concentration, the mixture was purified by silica gel column chromatography (Hexane:EtOAc = 3: 1, Rf = 0.52) to afford 8 (155 mg, 0.250 mmol, 81%). Molecular weight for C39H72Na05 (M+Na)+ Calc. 643.5277, Found 643.5273.
Compound 9: To a solution of compound 8 (150 mg, 0.242 mmol) and 4-(dimethylamino)butyric acid hydrochloride (49 mg, 0.290 mmol) in CH2C12 (5 mL) were added diisopropylethylamine (0.126 mL, 0.726 mmol), N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (56 mg, 0.290 mmol) and DMAP (6 mg, 0.0484 mmol). The reaction mixture was stirred at room temperature for 14 hours. The reaction mixture was then diluted with CH2C12 (100 mL) and washed with saturated NaHC03 aq. (50 mL). The organic layer was dried over MgS04, filtered and concentrated. The crude product was purified by silica gel column chromatography (0-5% MeOH in CH2C12) to afford compound 9 (121 mg, 0.165 mmol, 68%, Rf = 0.25 developed with 5% MeOH in CH2C12). Molecular weight for C45H84N06 (M+H)+ Calc. 734.6299, Found 734.5.
Compound 10: Treatment of compound 9 with CH C1 in CH CN and CHC13 can afford compound 10.
Example 2:
Scheme 2
Figure imgf000133_0001
Figure imgf000133_0002
Figure imgf000133_0003
Compound 12: To a solution of 11 (Journal of Medicinal Chemistry ( 1995), 38, 636-46; 1.25 g, 2.58 mmol) in THF (20 mL) and HMPA (4 mL), LiHMDS (1 M THF solution, 2.58 mL, 2.58 mmol) was added at -20 °C. The mixture was stirred for 20 min at the same temperature, then cooled to -78 °C. A solution of 4 (500 mg, 0.908 mmol) in THF (9 mL) and HMPA (0.9 mL) was added. The mixture was stirred from -78 °C to room temperature overnight. The reaction was quenched by adding H20 (40 mL) then extracted with Et20 (150 mL x 3). The organic layer was separated and dried over anhydrous Na2S04. After filtration and concentration, the crude was purified by silica gel column chromatography (Hexane:EtOAc = 9: 1, Rf = 0.35) to give 12 (136 mg, 0.169 mmol, 19%). Molecular weight for C5iH82Na05Si (M+Na)+ Calc. 825.5829, Found 825.5.
Using 13 in place of 5, a procedure analogous to that described for compound 7 was followed to afford compound 12 (135 mg, 0.168 mmol, 46%).
Compound 15/Compound 16: To a solution of 12 (800 mg, 0.996 mmol) in THF (5 mL), n- TBAF (1 M THF solution, 5 mL, 5.00 mmol) was added. The reaction mixture was stirred for 16 h at 45 °C. After concentration, the mixture was purified by silica gel column chromatography to give 15 (Hexane:EtOAc = 3: 1, Rf = 0.46, 372 mg, 0.659 mmol, 66%) and 16 (CH2Cl2:MeOH = 95:5, Rf = 0.36, 135 mg, 0.251 mmol, 25%). Molecular weight for 15; Css^NaOs (M+Na)+ Calc. 587.4651, Found 587.4652. Molecular weight for 16; C33H6105 (M+H)+ Calc. 537.4519, Found 537.5.
Compound 17: To a solution of compound 15 (164 mg, 0.290 mmol) and 4- (dimethylamino)butyric acid hydrochloride (58 mg, 0.348 mmol) in CH2C12 (5 mL) were added diisopropylethylamine (0.152 mL, 0.870 mmol), N-(3-dimethylaminopropyl)-N'- ethylcarbodiimide hydrochloride (67 mg, 0.348 mmol) and DMAP (7 mg, 0.058 mmol). The reaction mixture was stirred at room temperature for 14 hours. The reaction mixture was diluted with CH2C12 (100 mL) and washed with saturated NaHC03 aq. (50 mL). The organic layer was dried over MgS04, filtered and concentrated. The crude was purified by silica gel column chromatography (0-5% MeOH in CH2C12) to give compound 17 (158 mg, 0.233 mmol, 80%, Rf = 0.24 developed with 5% MeOH in CH2C12). Molecular weight for C45H84N06 (M+H)+ Calc. 734.6299, Found 734.5. Compound 18: Treatment of compound 17 with CH3C1 in CH CN and CHC13 can afford compound 18.
Compound 19: To a solution of 16 (130 mg, 0.242 mmol) in THF (2 mL) and MeOH (2 mL), trimethylsilyldiazomethane (2 M solution in Et20, 0.158 mL, 0.315 mmol) was added. The reaction mixture was stirred for 14 h. After evaporation, the residue was purified by silica gel column chromatography (Hexane:EtOAc = 3: 1, Rf = 0.50) to give 19 (99 mg, 0.180 mmol, 74%). 1H NMR (400 MHz, CDC13) δ 5.29-5.40 (m, 4 H), 4.12 (q, J = 7.1 Hz, 2 H), 3.66 (s, 3 H), 3.55- 3.59 (m, 1 H), 2.30 (dd, J = 14.7, 7.2 Hz, 4 H), 1.98-2.07 (m, 8 H), 1.60- 1.68 (m, 4 H), 1.23- 1.43 (m, 37 H).
Compound 20: To a solution of compound 19 (95 mg, 0.168 mmol) and 4- (dimethylamino)butyric acid hydrochloride (42 mg, 0.252 mmol) in CH2C12 (3 mL) were added diisopropylethylamine (0.088 mL, 0.504 mmol), N-(3-dimethylaminopropyl)-N'- ethylcarbodiimide hydrochloride (48 mg, 0.504 mmol) and DMAP (4 mg, 0.034 mmol). The reaction mixture was stirred at room temperature for 14 hours. The reaction mixture was diluted with CH2C12 (100 mL) and washed with saturated NaHC03 aq. (50 mL). The organic layer was dried over MgS04, filtered and concentrated. The crude was purified by silica gel column chromatography (0-5% MeOH in CH2C12) to give compound 20 (103 mg, 0.155 mmol, 92%, Rf = 0.19 developed with 5% MeOH in CH2C12). 1H NMR (400 MHz, CDC13) δ 5.29-5.40 (m, 4 H), 4.83-4.89 (m, 1 H), 4.12 (q, J = 7.1 Hz, 2 H), 3.67 (s, 3 H), 2.28-2.34 (m, 8 H), 2.23 (s, 6 H), 1.98-2.07 (m, 8 H), 1.76- 1.83 (m, 2 H), 1.60-1.68 (m, 4 H), 1.23-1.51 (m, 35 H).
Compound 21: Treatment of compound 20 with CH3C1 in CH3CN and CHC13 can afford compound 21. Example 3: Alternate Synthesis for Di- Aldehyde Intermediate 4
Scheme 3
22
(i) Mg/THF
(ii) HCOOEt
(iii) NaOH/EtOH
Figure imgf000136_0001
25
The di-aldehyde 4 can be synthesized as shown in Scheme 3, using l-bromo-9-decene. Di- aldehyde containing a head group 27 can be useful for the synthesis of terminal ester-substituted lipids using, e.g., a Wittig reaction. Ozonolysis can afford di-aldehyde 4 and 27.
Example 4: Alternate Synthesis for Compound 8
Scheme 4
BnBr _ _ _ ηΒη JDBn
PPh3/CH2CI2
29 30
1) Mg, MeOCHO ^ ho ~ - OBn TBSCI ^ /\/\^ΟΒη H2/Pd-C
2) NaBH4 0Bn TEA/CH2CI2 \^^~\/\/^0Bn H0Ac *
31 32 /\/OH MsCI MgBr2 Etherate
^oH TEA/CH2CI2 ^-^-^-^-OMs
33 34
Figure imgf000137_0001
Compound 8 can be synthesized as shown in Scheme 4.
Compound 29: To a stirred suspension of NaH (60% in oil, 82 g, 1.7096 mol) in 500mL anhydrous DMF, a solution of compound 28 (250 g, 1.7096 mol) in 1.5 L DMF was added slowly using a dropping funnel at 0 °C. The reaction mixture was stirred for 30 minutes, then benzyl bromide (208.86 mL, 1.7096 mol) was added slowly under an atmosphere of nitrogen.
The reaction was then warmed to ambient temperature and stirred for 10 hours. The mixture was then quenched with crushed ice (~2 kg) and extracted with ethyl acetate (2 x 1 L). The organic layer was washed with water (1L) to remove unwanted DMF, dried over Na2S04 and evaporated to dryness in vacuo. The crude compound was purified on 60-120 silica gel, eluted with 0-5% MeOH in DCM to afford compound 29 (220 g, 54%) as a pale yellow liquid. 1H NMR (400 MHz, CDC13): δ = 7.33-7.24 (m, 5 H), 4.49 (s, 2 H), 3.63-3.60 (m, 2 H), 3.47-3.43 (m, 2 H), 1.63-1.51 (m, 4 H), 1.39-1.23 (m, 8 H).
Compound 30: Compound 29 (133 g, 0.5635 mol) was dissolved in 1.5 L of DCM, CBr4 (280.35 g, 0.8456 mol) was added into this stirring solution and the reaction mixture was cooled to 0°C under an inert atmosphere. PPh3 (251.03 g, 0.9571 mol) was then added in portions keeping the temperature below 20 °C. After complete addition, the reaction mixture was stirred for 3 hours at room temperature. After completion of the reaction, the solid (PPh30) that precipitated from the reaction mixture was removed by filtration, and the filtrate was diluted with crushed ice (~ 1.5 kg) and extracted with DCM (3 x 750 mL). The organic layer was separated, dried over anhydrous Na2S04 and distilled under vacuum. The resulting crude compound was chromatographed on 60-120 mesh silica gel column using 0-5 % ethyl acetate in hexanes as eluting system to afford compound 30 (150 g, 89%) as pale yellow liquid. 1H NMR (400 MHz, CDC13): δ = 7.33-7.25 (m, 5 H), 4.49 (s, 2 H), 3.47-3.41 (m, 2 H), 3.41-3.37 (m, 2 H), 1.86-1.80 (m, 4 H), 1.62-1.56 (m, 2 H), 1.42-1.29 (m, 8 H).
Compound 31: To freshly activated Mg turnings (24.08 g, 1.003 mol) was added 200 mL anhydrous THF, followed by the addition of pinch of iodine into the mixture under an inert atmosphere. A solution of Compound 30 (150 g, 0.5016 mol) in 1 L of dry THF was added slowly, controlling the exothermic reaction. The reaction was then heated to reflux for 1 hour, then cooled to room temperature. Methyl formate (60.24 g, 1.0033 mol) was then added slowly and the reaction was continued for 2 hours. After completion, the reaction was quenched by slow addition of 10% HC1 followed by water (1 L) and extracted with ethyl acetate (3 x 1 L). The organic layer was taken in 5 litre beaker, diluted with 500 mL of methanol and cooled to 0 °C. To this solution, an excess of NaBH4 (~ 5eq) was added in portions to ensure hydrolysis of the formate ester which was not cleaved by addition of HC1. The resulting solution was stirred for an hour and then volatilites were removed under vacuum. The residue was taken in water (1 L) and acidified by 10% HC1 solution (pH 4). The product was then extracted with ethyl acetate (3 x 1 L). the organic phase was then dried and concentrated on rotary evaporator to afford the desired compound 31 (57 g, 24%) as solid. 1H NMR (400 MHz, CDC13): δ = 7.35-7.32 (m, 8 H), 7.29- 7.24 (m, 2 H), 4.49 (s, 4 H), 3.56 (m, 1 H), 3.46-3.43 (m, 4 H), 1.63-1.56 (m, 4 H), 1.44-1.34 (m, 28 H). 13C NMR (100 MHz, CDC13): δ = 138.56, 128.21, 127.49, 127.34, 72.72, 71.76, 70.37, 37.37, 29.64, 29.56, 29.47, 29.33, 26.07, 25.54.
Compound 32: Compound 31 (56 g, 0.1196 mol) was dissolved in 700 mL dry THF and cooled to 0 °C. TBSC1 (36.06 g, 0.2396 mol) was added slowly followed by the addition of imidazole (32.55 g, 0.4786 mol) under an inert atmosphere. The reaction was then stirred at room temperature for 18 hours. Upon completion, the reaction was quenched with ice (~1 kg) and extracted with ethyl acetate (3 x 500 mL). The organic layer was separated, washed with saturated NaHC03 solution to remove acidic impurities, dried over Na2S04 and evaporated under reduce pressure to afford a crude compound that was purified by silica gel (60-120 mesh) and eluted with 0- 10% ethyl acetate hexane to afford (60 g, 82%) of compound 32 as yellowish oil. 1H NMR (400 MHz, CDC13): δ = 7.33-7.24 (m, 10 H), 4.49 (s, 4 H), 3.60-3.57 (m, 1 H), 3.46- 3.43 (m, 4 H), 1.61-1.54 (m, 4 H), 1.41-1.26 (m, 28 H), 0.87 (s, 9 H), 0.02 (s, 6 H).
Compound 33: Compound 32 (60 g, 0.1030 mol) was dissolved in 500 mL ethyl acetate and degassed with N2 for 20 minutes. (10 wt %) Pd on carbon (12 g) was added and the reaction was stirred under an atmosphere of hydrogen for 18 hours. After completion, the mixture was filtered through a bed of celite and washed with ethyl acetate. The filtrate was evaporated under vacuum to afford compound 33 (19 g, 46%) that was pure enough to use in the next synthetic sequence. 1H NMR (400 MHz, CDC13): δ = 3.64-3.58 (m, 5 H), 1.59 (br, 2 H), 1.57-1.51 (m, 4 H), 1.38- 1.22 (m, 28 H), 0.87 (s, 9 H), 0.02 (s, 6 H).
Compound 34: Compound 33 (8.2 g, 0.0199 mol) was dissolved in 100 mL dry DCM and cooled to 0 °C. TEA (22.14 mL, 0.1592 mol) was added under an inert atmosphere. After stirring the mixture for 5 minutes, mesyl chloride (4.6 mL, 0.059 mol) was added drop wise and the reaction was stirred further for 3 hours. After completion of the reaction, the mixture was quenched with ice (-200 g) and extracted with DCM (3 x 75 mL). The organic layer was dried over anhydrous sodium sulfate and evaporated to afford a crude compound which was purified on a 60-120 mesh silica gel column using 0-30% ethyl acetate in hexane as eluting system to afford compound 34 (8.2 g, 73%) as a pale yellow liquid. 1H NMR (400 MHz, CDC13): δ = 4.22-4.19 (m, 4 H), 3.60-3.58 (m, 1 H), 2.99 (s, 6 H), 1.75-1.69 (m, 4 H), 1.38-1.28 (m, 28 H), 0.86 (s, 9 H), 0.02 (s, 6 H).
Compound 35: To a solution of compound 34 (8.2 g, 0.0146 mol) in 400 mL dry ether was added MgBr2 Et20 (22.74 g, 0.08817 mol) in portions at 0 °C under a nitrogen atmosphere. After complete addition, the reaction mixture was heated to reflux for 28 hours. After completion of reaction, inorganic material formed in the reaction was removed by filtration. The filtrate was evaporated and the resulting crude compound was purified on 60-120 mesh silica gel column using 0-3% ethyl acetate in hexanes as eluting system to afford compound 35 (6.6 g, 85%) as a colorless liquid. 1H NMR (400 MHz, CDC13): δ = 3.61-3.58 (m, 1 H), 3.41-3.37 (t, 4 H, J = 6.8 Hz), 1.87-1.80 (m, 4 H), 1.42-1.25 (m, 24 H), 0.87 (s, 9 H), 0.012 (s, 6 H).
Compound 36: A solution of ethynyl trimethyl silane (5.3 mL, 0.0378 mol) in 60 mL dry THF was cooled to -78°C and 1.4 M w-BuLi (23 mL, 0.03405 mol) in hexane was added slowly under an inert atmosphere. The reaction was stirred for 10 minutes, then HMPA (2.3 g, 0.01324 mol) was added and the resulting mixture was then stirred for 2 hours at 0 °C, then cooled to -78 °C. To this a solution of compound 35 (5 g, 0.0094 mol) in 60 mL dry THF was added slowly and after complete addition, the reaction was warmed to room temperature and maintained for 18 hours. The reaction progress was monitored by 1H NMR. After completion, the reaction mixture was cooled to 0 °C and quenched by careful addition of saturated NH4C1 solution (50 mL) followed by water (200 mL). The aqueous phase was extracted with hexane (3 x 250 mL). The organic layer was dried and solvent removed under vacuum to afford compound 36 (5 g, 94%), which was used without further purification. 1H NMR (400 MHz, CDC13): δ = 3.62-3.56 (m, 1 H), 2.21-2.17 (m, 4 H), 1.49-1.47 (m, 4 H), 1.37-1.26 (m, 24 H), 0.87 (s, 9 H), 0.13 (s, 18 H), 0.021 (s, 6 H).
Compound 37: To a stirred solution of compound 36 (5 g, 0.0088 mol) in 50 mL methanol, was added K2C03 (6.1 g, 0.044 mol) in one portion, and the resulting mixture was stirred for 18 hours at ambient temperature. Volatilities were then removed on a rotary evaporator and the crude mixture was diluted with 100 mL water and extracted with hexane (3 x 100 mL). The organic layer was dried over Na2S04 and evaporated under vacuum to afford compound 37 (3.5 g, 97%) which was used which was used without further purification. 1H NMR (400 MHz, CDC13): δ = 3.60-3.58 (m, 1 H), 2.19-2.14 (m, 4 H), 1.93-1.92 (m, 2 H), 1.54-1.49 (m, 4 H), 1.37-1.27 (m, 24 H), 0.87 (s, 9 H), 0.02 (s, 6 H).
Compound 39: Compound 37 (2.5 g, 0.00598 mol) was dissolved in 25 mL dry THF and cooled to -40 °C. w-BuLi (1.4 M in hexane 12.9 mL, 0.01794 mol) was added slowly, followed, after a 10 minute interval, by slow addition of HMPA (25 mL). The resulting mixture was maintained for 30 minutes -40 °C under a nitrogen atmosphere. A solution of compound 38 (3.5 g, 1.01196 mol) in 25 mL dry THF was then added drop wise to the cooled reaction mixture. The resulting mixture was warmed to room temperature over 2 hours, then stirred at room temperature for 18 hours. The mixture was then quenched by adding saturated NH4C1 solution (-50 mL) and the product was extracted with ethyl acetate (3 x 50 mL). The solvent was removed on a rotary evaporator and the resulting crude product was purified by (100-200 mesh) silica gel column using 0-3% ethyl acetate in dichloromethane as eluting system to afford compound 39 (0.9 g, 18%) as a yellow oil. 1H NMR (400 MHz, CDC13): δ = 4.56-4.55 (m, 2 H), 3.87-3.83 (m, 2 H), 3.74-3.68 (m, 2 H), 3.59-3.57 (m, 1 H), 3.49-3.46 (m, 2 H), 3.39-3.33 (m, 2 H), 2.13-2.10 (m, 8 H), 1.87-1.75 (m, 2 H), 1.74-1.66 (m, 2 H), 1.57-1.42 (m, 20 H), 1.40-1.19 (m, 40 H), 0.87 (s, 9 H), 0.02 (s, 6 H).
Compound 40: To a solution of compound 39 (504 mg, 0.598 mmol) in 10 mL dry ether was added MgBr2 Et20 (926 mg, 3.59 mmol). The reaction mixture was stirred for 14 hours, then quenched by adding saturated NaHC03 aqueous solution. The product was extracted with CH2C12. The organic layer was dried over Na2S04, filtered and concentrated. The crude product was purified by silica gel column chromatography to afford compound 40 (307 mg, 0.455 mmol, 76%, Rf = 0.36 developed with hexane:EtOAc = 2: 1). 1H NMR (400 MHz, CDC13) δ 3.59-3.66 (m, 5 H), 2.14 (t, J = 6.6 Hz, 8 H), 1.21-1.59 (m, 52 H), 0.88 (s, 9 H), 0.03 (s, 6 H).
Compound 41: To a stirred solution of 40 (180 mg, 0.267 mmol) in anhydrous DMF (5 mL) was added pyridinium dichromate (603 mg, 1.60 mmol). The reaction mixture was stirred for 48 hours. After dilution with water (20 mL), the mixture was extracted with Et20 (3 x 40 mL). The organic layer was dried over Na2S04, filtered and concentrated. The crude product was purified by silica gel column chromatography to afford compound 41 (53 mg, 0.075 mmol, 28%, Rf = 0.25 developed with CH2Cl2:MeOH:AcOH = 95:4.5:0.5). Molecular weight for C43H77O5S1 (M- H)" Calc. 701.5540, Found 701.5. This compound can be synthesized by TEMPO oxidation.
Compound 42: A procedure analogous to that described for compound 19 afforded compound 42 (23 mg 0.032 mmol, 21 % from compound 40). 1H NMR (400 MHz, CDC13) δ 3.67 (s, 6 H), 3.59-3.62 (m, 1 H), 2.30 (t, J = 1.5 Hz, 4 H), 2.13 (t, J = 6.8 Hz, 8 H), 1.27-1.64 (m, 48 H), 0.88 (s, 9 H), 0.03 (s, 6 H).
Reduction using P-2 nickel conditions can give compound 43 and subsequent deprotection by TBAF can afford compound 8.
Example 5: Alternate Synthesis for Compound 8
Scheme 5
Figure imgf000142_0001
Figure imgf000142_0002
Compound 8 can be synthesized as shown in Scheme 5. The bromide 51 can be converted to its Grignard reagent then coupled with ethyl formate to afford compound 52. Subsequent acid treatment, oxidation, and reduction can give compound 8. Example 6: Alternate Synthesis for Compound 8
Scheme 6
Figure imgf000143_0001
Compound 8 can be synthesized as shown in Scheme 6. Either bromides of compound 58, 60, or 62 can be reacted with ethyl formate to generate terminal-functionalized di-olefin chain.
Compound 8 can then be prepared from the diolefin chain compounds using standard chemical reactions.
Example 7: General synthetic scheme for terminal ester lipids
Scheme 7
Figure imgf000144_0001
Figure imgf000144_0002
As shown in Scheme 7, chain length and linker length as well as alkyl groups in ester functionality and substituents on nitrogen atom can be derivatized.
Example 8: General synthetic scheme 2 for terminal ester lipids
Scheme 8
Figure imgf000144_0003
As shown in Scheme 8, copper-mediated coupling affords di-yne containing lipid chain with terminal functional groups, which can be easily reduced to generate di-ene containing lipid chains. The length of linker and lipid chain as well as functional substituent groups (R, R1; R2) can be derivatized.
Example 9: Synthesis of terminal benzyl ester lipid
Scheme 9
Figure imgf000145_0001
Compound 201: Compound 7 (1.30 g, 1.51 mmol) was treated with lithium hydroxide monohydrate (317 mg, 7.55 mmol) in THF (25 mL) and H20 (5 mL) for 12 h. Amberlite IR-120 (plus) ion exchange resin was added then stirred for 10 minutes. The resulting clear solution was filtered, washed with THF/H20 and evaporated. Co-evaporation with toluene gave the compound 201 (1.22 g, 1.47 mmol, 97%). Molecular weight for C53H8505Si (M-H)" Calc. 829.6166, Found 829.5.
Compound 202: A procedure analogous to that described for compound 9 was followed with benzylalcohol and 201 (101 mg, 0.121 mmol) to afford compound 202 (87 mg, 0.0860 mmol, 71%). 1H NMR (400 MHz, CDC13) δ 7.68 - 7.66 (m, 4 H), 7.42 - 7.30 (m, 16 H), 5.38 - 5.30 (m, 4 H), 5.11 (s, 4 H), 3.71 - 3.68 (m, 1 H), 2.35 (t, J = 7.6 Hz, 4 H), 2.04 - 1.97 (m, 8 H), 1.66 - 1.62 (m, 4 H), 1.40 - 1.07 (m, 44 H), 1.04 (s, 9 H). Compound 203: A procedure analogous to that described for compound 8 was followed with 202 (342 mg, 0.338 mmol) to afford compound 202 (136 mg, 0.176 mmol, 52%). 1H NMR (400 MHz, CDC13) δ 7.38 - 7.30 (m, 10 H), 5.38 - 5.30 (m, 4 H), 5.11 (s, 4 H), 3.57 (brs, 1 H), 2.35 (t, J = 7.6 Hz, 4 H), 2.01 - 1.98 (m, 8 H), 1.66 - 1.60 (m, 4 H), 1.45 - 1.25 (m, 44 H).
Compound 204: A procedure analogous to that described for compound 9 was followed with 203 (133 mg, 0.172 mmol) to afford compound 204 (93 mg, 0.105 mmol, 61%). 1H NMR (400 MHz, CDCI3) δ 7.38 - 7.26 (m, 10 H), 5.38 - 5.30 (m, 4 H), 5.11 (s, 4 H), 4.88 - 4.83 (m, 1 H), 2.37 - 2.27 (m, 8 H), 2.22 (s, 6 H), 2.03 - 1.97 (m, 8 H), 1.81 - 1.26 (m, 50 H).
Example 10: Synthesis of terminal t-butyl ester lipid and the derivatives
Scheme 10
Figure imgf000146_0001
Compound 206: A procedure analogous to that described for compound 12 was followed with 205 (3.80 g, 0.7.61 mmol) and 4 (1.75 g, 3.17 mmol) to afford compound 206 (2.00 g, 2.12 mmol, 67%). 1H NMR (400 MHz, CDC13) δ 7.68 - 7.66 (m, 4 H), 7.42 - 7.33 (m, 6 H), 5.39 - 5.31 (m, 4 H), 3.71 - 3.68 (m, 1 H), 2.20 (t, J = 7.6 Hz, 4 H), 2.01 - 1.98 (m, 8 H), 1.59 - 1.55 (m, 4 H), 1.44 (s, 18 H), 1.41 - 1.11 (m, 44 H), 1.04 (s, 9 H).
Compound 207: A procedure analogous to that described for compound 8 was followed with 206 (265 mg, 0.281 mmol) to afford compound 207 (161 mg, 0.228 mmol, 81%). 1H NMR (400 MHz, CDC13) δ 5.38 - 5.30 (m, 4 H), 3.58 (brs, 1 H), 2.20 (t, J = 7.4 Hz, 4 H), 2.01 - 1.98 (m, 8 H), 1.59 - 1.55 (m, 4 H), 1.44 (s, 18 H), 1.35 - 1.26 (m, 44 H).
Compound 208: A procedure analogous to that described for compound 9 was followed with 207 (158 mg, 0.224 mmol) to afford compound 208 (138 mg, 0.169 mmol, 75%). Molecular weight for C5iH96N06 (M+H)+ Calc. 818.7238, Found 818.7.
Compound 209: Compound 208 (148 mg, 0.181 mmol) was treated with TFA (1.5 mL) in CH2CI2 (6 mL) for 2.5 h. After evaporation and co-evaporation with toluene gave the compound 209 (154 mg, quant.). Molecular weight for C43H8oN06 (M+H)+ Calc. 706.5980, Found 706.5.
Compound 210: A procedure analogous to that described for compound 9 was followed with 209 (0.061 mmol) and ci5,-2-Hexen-l-ol (18.3 mg, 0.183 mmol) to afford compound 210 (32 mg, 0.0368 mmol, 60%). Molecular weight for C55H100NO6 (M+H)+ Calc. 870.7551, Found 870.5.
Example 11: Synthesis of internal ester/amide lipids-1
Scheme 11
Figure imgf000148_0001
= 1 (217), 66%
= 3 (219), 66%
Compound 213: Compound 211 (503 mg, 1.0 mmol) was treated with 212 (533 mg, 3.0 mmol) in CH2CI2 (35 mL) and DIPEA (1.74 mL, 10 mmol) for 14 h. Aqueous work-up then column chromatography gave compound 213 (506 mg, 0.748 mmol, 75%). Molecular weight for C41H78N3O4 (M+H)+ Calc. 676.5992, Found 676.4.
Compound 215: Compound 211 (503 mg, 1.0 mmol) was treated with 214 (469 mg, 3.0 mmol) and K2CO3 (1.38 g, 10 mmol) in CH2CI2 (35 mL) for 14 h. Aqueous work-up then column chromatography gave compound 215 (244 mg, 0.346 mmol, 35%). Molecular weight for C43H8oN06 (M+H)+ Calc. 706.5986, Found 706.4.
Compound 217: Compound 211 (425 mg, 0.845 mmol) was treated with 216 (525 mg, 3.08 mmol) and K2C03 (1.17 g, 8.45 mmol) in CH2CI2 (35 mL) for 14 h. Aqueous work-up then column chromatography gave compound 217 (407 mg, 0.554 mmol, 66%). Molecular weight for C45H84N06 (M+H)+ Calc. 734.6299, Found 734.4. Compound 219: Compound 211 (503 mg, 1.0 mmol) was treated with 218 (595 mg, 3.0 mmol) and K2CO3 (1.38 g, 10 mmol) in CH2CI2 (35 mL) for 14 h. Aqueous work-up then column chromatography gave compound 219 (519 mg, 0.657 mmol, 66%). Molecular weight for C49H92NO6 (M+H)+ Calc. 790.6925, Found 790.7.
Example 12: Synthesis of internal ester lipid-223
Figure imgf000149_0001
Compound 221: A procedure analogous to that described for compound 9 was followed with 220 (390 mg, 1.93 mmol) and 218 (765 mg, 3.86 mmol) to afford compound 221 (878 mg, 1.56 mmol, 81%). 1H NMR (400 MHz, CDC13) δ 5.67 - 5.61 (m, 2 H), 5.54 - 5.48 (m, 2 H), 4.62 (d, J = 6.8 Hz, 4 H), 2.47 (t, J = 7.2 Hz, 4 H), 2.33 (t, J = 7.2 Hz, 4 H), 2.12 - 2.06 (m, 4 H), 1.93 - 1.86 (m, 4 H), 1.38 - 1.26 (m, 32 H), 0.88 (t, J = 6.8 Hz, 6 H).
Compound 222: Compound 221 (318 mg, 0.565 mmol) was treated with NaBH(OAc)3 (360 mg, 1.70 mmol) in CH2CI2 (5 mL) and AcOH (0.2 mL) for 16 h. After evaporation, column chromatography gave compound 222 (141 mg, 0.250 mmol, 44%). Molecular weight for
C35H6505 (M+H)+ Calc. 565.4832, Found 565.4. Compound 223: A procedure analogous to that described for compound 9 was followed with 222 (137 mg, 0.243 mmol) to afford compound 223 (137 mg, 0.202 mmol, 83%). Molecular weight for C4iH76N06 (M+H)+ Calc. 678.5673, Found 678.5.
Example 13: Synthesis of internal ester lipid-227
Scheme 13
Figure imgf000150_0001
Compound 225: A procedure analogous to that described for compound 9 was followed with 224 (200 mg, 0.774 mmol) and 216 (264 mg, 1.55 mmol) to afford compound 225 (341 mg, 0.606 mmol, 78%). Molecular weight for CssHeiNaOs (M+Na)+ Calc. 585.4495, Found 585.5.
Compound 226: Compound 225 (283 mg, 0.503 mmol) was treated with NaBH4 (57 mg, 1.51 mmol) in THF (5 mL) and AcOH (0.2 mL) for 8 h. After evaporation, column chromatography gave compound 226 (185 mg, 0.328 mmol, 65%). Molecular weight for C35H64Na05 (M+Na)+ Calc. 587.4651, Found 587.3. Compound 227: A procedure analogous to that described for compound 9 was followed with 226 (230 mg, 0.407 mmol) to afford compound 227 (248 mg, 0.366 mmol, 90%). Molecular weight for C4iH76N06 (M+H)+ Calc. 678.5673, Found 678.5.
Example 14: Synthesis of terminal ester lipid with linoleyl chain-232
Scheme 14
Figure imgf000151_0001
Compound 230: A procedure analogous to that described for compound 7 was followed with 228 (3.27 g, 6.0 mmol) and 4 (1.27 g, 2.30 mmol) to afford compound 230 (1.31 g, 1.53 mmol, 67%). 1H NMR (400 MHz, CDC13) δ 7.68 - 7.66 (m, 4 H), 7.42 - 7.33 (m, 6 H), 5.42 - 5.29 (m, 8 H), 3.71 - 3.68 (m, 1 H), 3.66 (s, 6 H), 2.77 (t, J = 5.8 Hz, 4 H), 2.33 - 2.28 (m, 4 H), 2.11 - 2.01 (m, 8 H), 1.69 - 1.60 (m, 4 H), 1.43 - 1.10 (m, 32 H), 1.04 (s, 9 H).
Compound 231: A procedure analogous to that described for compound 8 was followed with 230 (1.30 g, 1.52 mmol) to afford compound 231 (611 mg, 0.990 mmol, 65%). 1H NMR (400 MHz, CDC13) δ 5.41 - 5.29 (m, 8 H), 3.67 (s, 6 H), 3.58 (brs, 1 H), 2.77 (t, J = 5.8 Hz, 4 H), 2.32 (t, J = 7.4 Hz, 4 H), 2.10 - 2.00 (m, 8 H), 1.69 - 1.60 (m, 4 H), 1.43 - 1.29 (m, 32 H). Compound 232: A procedure analogous to that described for compound 9 was followed with 231 (520 mg, 0.843 mmol) to afford compound 232 (600 mg, 0.822 mmol, 97%). Molecular weight for C45H8oN06 (M+H)+ Calc. 730.5986, Found 730.5.
Example 15: Synthesis of terminal ester lipid with linoleyl chain-232
Scheme 15
Figure imgf000152_0001
Compound 231 was also synthesized as shown Scheme 15.
Compound 112: Compound 111 (840 mg, 2.69 mmol) was treated with dimethyl (l-diazo-2- oxopropyl)phosphonate (0.970 mL, 6.46 mmol) and K2C03 (1.49 g, 10.8 mmol) in MeOH (40 mL) for 6 h. Aqueous work-up then column chromatography gave compound 112 (700 mg, 2.30 mmol, 86%). 1H NMR (400 MHz, CDC13) δ 3.58 (brs, 1 H), 2.18 (td, J = 7.1, 2.6 Hz, 4 H), 1.94 (t, J = 2.6 Hz, 2 H), 1.56 - 1.25 (m, 28 H).
Compound 234: Compound 112 (207 mg, 0.680 mmol) was treated with 233 (316 mg, 1.36 mmol), K2C03 (282 mg, 2.04 mmol), Nal (408 mg, 2.72 mmol) and Cul (518 mg, 2.72 mmol) in DMF (3.5 mL) for 18 h. Aqueous work-up then column chromatography gave compound 234 (292 mg, 0.480 mmol, 71%). Molecular weight for C39H6105 (M+H)+ Calc. 609.4519, Found 609.5.
Compound 231: To a stirred solution of nickel(II) acetate tetrahydrate (533 mg, 2.14 mmol) in EtOH (28.5 mL), 1 M solution of NaBH4 in EtOH (2.14 mL) was added at room temperature. After 30 min, ethylenediamine (0.574 mL, 8.57 mmol) and a solution of 234 (290 mg, 0.476 mmol) in EtOH (3 mL) was added then stirred for 1 h. The reaction mixture was filtered through Celite and evaporated. Aqueous work-up then column chromatography gave compound 231 (219 mg, 0.355 mmol, 75%). Molecular weight for C39H6905 (M+H)+ Calc. 617.5145, Found 617.3.
Example 16: Synthesis of internal oxime lipid-238
Scheme 16
Figure imgf000153_0001
Compound 237: Compound 235 (465 mg, 1.78 mmol) was treated with hydrazine monohydrate (64-65%, 0.135 mL, 1.78 mmol) in EtOH (15 mL) for 4 h. After filtration then evaporation, the crude was re-suspended in EtOH (5 mL). To this solution was added compound 111 (160 mg, 0.512 mmol) and AcOH (a few drops). Aqueous work-up then column chromatography gave compound 237 (165 mg, 0.306 mmol, 60%). Molecular weight for C33H67N203 (M+H)+ Calc. 539.5152, Found 539.3.
Compound 238: A procedure analogous to that described for compound 9 was followed with 237
(162 mg, 0.301 mmol) to afford compound 238 (168 mg, 0.258 mmol, 86%). Molecular weight for C39H78N304 (M+H)+ Calc. 652.5992, Found 652.4. Example 17
Scheme 17:
Figure imgf000154_0001
ALNY-319
8-benzyloxy-octan-l-ol (240): To a stirred suspension of NaH (60% in oil, 82 g, 1.7096 mol) in
500mL anhydrous DMF, a solution of compound 239 (250g, 1.7096 mol) in 1.5 L DMF was added slowly using a dropping funnel at 0° C. The reaction mixture was stirred for 30 minutes, then benzyl bromide (208.86 mL, 1.7096 mol) was added slowly under a nitrogen atmosphere.
The reaction was then warmed to ambient temperature and stirred for 10 hours. After completion of reaction, the mixture was quenched with crushed ice (~2kg) and extracted with ethyl acetate
(2 x IL). The organic layer washed with water (IL) to remove unwanted DMF, dried over Na2S04 and evaporated to dryness under vacuum. The crude compound was purified on 60-120 silica gel, eluted with 0-5% MeOH in DCM to afford compound 240 (220g, 54%) as pale yellow liquid. H1 NMR (400MHz, CDC13): δ = 7.33-7.24 (m, 5H), 4.49 (s, 2H), 3.63-3.60 (m, 2H), 3.47- 3.43 (m, 2H), 1.63-1.51 (m, 4H), 1.39-1.23 (m, 8H).
(8-bromo-octyloxymethyl)-benzene (241): Compound 240 (133g, 0.5635mol) was dissolved in 1.5 L of DCM, CBr4 (280.35g, 0.8456mol) was added to this stirring solution and the reaction mixture was cooled to 0°C under an inert atmosphere. PPh3 (251.03g, 0.957 lmol) was then added in portions maintaining the temperature below 20°C and after complete addition, the reaction mixture was stirred for 3 hours at room temperature. After completion of reaction, solid (PPh30) precipitated out from the reaction mixture was isolated by filtrationand the filtrate was diluted with crushed ice (~ 1.5kg) and extracted with DCM (3 x 750mL). The organic layer was separated, dried over anhydrous Na2S04 and distilled under vacuum. The resulting crude compound was chromatographed on 60-120 mesh silica gel column using 0-5 % ethyl acetate in hexanes as eluting system to afford compound 241 (150g, 89%) as pale yellow liquid. 1H NMR (400MHz, CDC13): δ = 7.33-7.25 (m, 5H), 4.49 (s, 2H), 3.47-3.41 (m, 2H), 3.41-3.37 (m, 2H), 1.86-1.80 (m, 4H), 1.62-1.56(m, 2H), 1.42-1.29 (m, 8H).
1, 17-bis-benzyloxy-heptadecan-9-ol (242): To freshly activated Mg turnings (24.08g, 1.003mol) was added 200mL anhydrous THF, followed by the addition of pinch of iodine into the mixture under inert atmosphere. After initiation of the Grignard formation a solution of Compound 241 (150g, 0.5016mol) in 1 L of dry THF was added slowly controlling the exothermic reaction. After complete addition, the reaction was heated to reflux for 1 hour, then cooled to room temperature. Methyl formate (60.24g, 1.0033mol) was then added slowly and reaction was continued for 2 hours. After completion, the reaction was quenched by slow addition of 10% HCl followed by water (1 L) and extracted with ethyl acetate (3 x 1L). The organic layer was taken in 5 litre beaker, diluted with 500mL of methanol and cooled to 0°C. To this solution excess of NaBH4 (~ 5eq) was added in portions to ensure the hydrolysis of formate ester which was not cleaved by addition of HCl. The resulting solution was stirred for an hour and then volatilites were removed under vacuum. The residue was taken in water (1 L) and acidified by 10% HCl solution (P 4). The product was then extracted with ethyl acetate (3 x 1 L). The organic phase was then dried and concentrated on rotary evaporator to afford compound 242 (57g, 24%) as solid. 1H NMR (400MHz, CDC13): δ = 7.35-7.32 (m, 8H), 7.29-7.24 (m, 2H), 4.49 (s, 4H), 3.56 (m, 1H), 3.46-3.43 (m, 4H), 1.63-1.56 (m, 4H), 1.44-1.34 (m, 28H). C13 NMR (100MHz, CDC13): δ = 138.56, 128.21, 127.49, 127.34, 72.72, 71.76, 70.37, 37.37, 29.64, 29.56, 29.47, 29.33, 26.07, 25.54.
[9-benzyloxy-l-(8-benzylozy-octyl)-nonyloxy]-tert-butyl-dimethyl-silane (243): Compound 242 (56 g, 0.1196 mol) was dissolved in 700 mL of anhydrous THF and cooled to 0 °C. TBMS- Cl (36.06g, 0.2396mol) was added slowly followed by addition of imidazole (32.55 g, 0.4786 mol) under an inert atmosphere. The reaction was then stirred at room temperature for 18 hours, then quenched with ice (~lkg). The product was extracted with ethyl acetate (3 x 500mL). The organic layer was separated, washed with saturated NaHC03 solution to remove the acidic impurity, dried over Na2S04 and evaporated under reduce pressure to obtain crude compound which was purified by silica gel (60-120 mesh) and eluted with 0- 10% ethyl acetate hexane to afford (60g, 82%) of compound 243 as yellowish oil. H1 NMR (400MHz, CDC13): δ = 7.33-7.24 (m, 10H), 4.49 (s, 4H), 3.60-3.57 (m, 1H), 3.46-3.43 (m, 4H), 1.61-1.54 (m, 4H), 1.41-1.26 (m, 28H), 0.87 (s, 9H), 0.02 (s, 6H)
9-(tert-butyl-dimethyl-silanyloxy)-heptadecane-l, 17-diol (244): Compound 243 (60 g, 0.1030 mol) was dissolved in 500mL ethyl acetate and degassed with N2 for 20 min. (10 wt %) Pd on carbon (12 g) was added and reaction was stirred under an atmosphere of hydrogen for 18 hours. After completion, the mixture was filtered through a bed of celite and washed with ethyl acetate. The filtrate was evaporated under vacuum. Compound 244 (19 g, 46%) thus obtained was pure enough to carry out the next reaction. 1H NMR (400MHz, CDC13): δ = 3.64-3.58 (m, 5H), 1.59 (br, 2H), 1.57-1.51 (m, 4H), 1.38-1.22 (m, 28H), 0.87 (s, 9H), 0.02 (s, 6H).
9-(tert-butyl-dimethyl-silanyloxy)-heptadecanedioic acid (245): To a stirred solution of 244 (2 g, 0.0049 mol) in anhydrous DMF (40 mL) was added pyridinium dirchromate (2.7 g, 0.0074 mol) at 0 °C under an inert atmosphere. The reaction mixture was then allowed to warm to room temperature over a period of 10-15 minutes and continued for 24 hours. Then, the reaction was diluted with water (lOOmL). The aqueous phase was extracted using DCM (3 x 40mL). The organic phase was washed with brine (lx 25mL) and concentrated under vacuum to afford crude acid which was then purified by (100-200 mesh) silica gel column using 0-30% ethyl acetate in hexanes system. Pure product (245) was obtained (0.7g, 33%) as a pale yellow oil. 1H NMR (400MHz, CDC13): δ = 3.61-3.56 (m, 1H), 2.35-2.32 (m, 4H), 1.64- 1.59 (m, 4H), 1.40- 1.19 (m, 24H), 0.86 (s, 9H), 0.017 (s, 6H); LC-MS [M+H] - 431.00; HPLC (ELSD) purity - 96.94%
Di((Z)-non-2-en-l-yl) 9-((tert-butyldimethylsilyl)oxy)heptadecanedioate (246): The diacid 245 (0.42 g, 0.97 mmol) was dissolved in 20 mL of dichloromethane and to it ds^-nonen-l-ol (0.35 g, 2.44 mmol) was added followed by Hunig's base (0.68 g, 4.9 mmol) and DMAP (12 mg). To this mixture EDCI (0.47 g, 2.44 mmol) was added and the reaction mixture was stirred at room temperature overnight. The reaction mixture was then diluted with CH2CI2 (40 mL) and washed with saturated NaHC03 (50 mL), water (60 mL) and brine (60 mL). The combined organic layers were dried over anhydrous Na2S04 and solvents were removed in vacuo. The crude product thus obtained was purified by Combiflash Rf purification system (40 g silicagel, 0- 10 % MeOH in CH2C12) to afford the pure product 246 (0.35 g, 53%) as a colorless oil. 1H NMR (400 MHz, CDC13): δ 1H NMR (400 MHz, CDC13) δ 5.64 (dt, J = 10.9, 7.4 Hz, 2H), 5.58 - 5.43 (m, 2H), 4.61 (d, J = 6.8 Hz, 4H), 3.71 - 3.48 (m, 1H), 2.30 (t, J = 7.6 Hz, 4H), 2.20 - 1.98 (m, 4H), 1.71 - 1.53 (m, 4H), 1.31 (ddd, J = 8.3, 7.0, 3.7 Hz, 34H), 1.07 - 0.68 (m, 14H), 0.02 (s, 5H). 13C NMR (101 MHz, CDC13) δ 178.18, 139.81, 127.78, 81.73, 81.42, 81.10, 76.72, 64.59, 41.52, 41.32, 38.76, 36.09, 34.10, 33.93, 33.80, 33.70, 33.59, 33.55, 33.26, 31.95, 30.34, 29.69, 29.58, 29.39, 27.01, 22.56, 18.48, 0.01.
Di((Z)-non-2-en-l-yl) 9-hydroxyheptadecanedioate (247): The silyl protected diester 246 (0.3 g, 0.44 mmol) was dissolved in 1 M solution of TBAF in THF (6 mL) and the solution was kept at 40 °C for two days. The reaction mixture was diluted with water (60 mL) and extracted with ether (2 x 50 mL). The combined organic layers were concentrated and the thus obtained crude product was purified by column to isolate the pure product (0.097 g, 39%). 1H NMR (400 MHz, CDC13) δ 5.64 (dt, J = 10.9, 7.4 Hz, 2H), 5.52 (dt, J = 11.0, 6.8 Hz, 2H), 4.61 (d, J = 6.8 Hz, 4H), 3.57 (s, 1H), 2.30 (t, J = 7.5 Hz, 4H), 2.09 (q, J = 7.1 Hz, 4H), 1.75 - 1.53 (m, 4H), 1.53 - 1.06 (m, 36H), 0.88 (t, J = 6.8 Hz, 6H). 13C NMR (101 MHz, CDC13) δ 173.98, 135.64, 123.57, 77.54, 77.22, 76.91, 72.14, 60.41, 37.69, 34.54, 31.89, 29.70, 29.60, 29.44, 29.29, 29.07, 27.76, 25.80, 25.15, 22.82, 14.29.
Di((Z)-non-2-en-l-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate: The alcohol 247 (0.083 g, 0.147 mmol) was dissolved in 20 mL of dichloromethane and to it dimethylaminobutyric acid hydrochloride (0.030 g, 0.176 mmol) was added followed by Hunig's base (0.045 g, 0.44 mmol) and DMAP (2 mg). To this mixture EDCI (0.034 g, 0.176 mmol) was added and the reaction mixture was stirred at room temperature overnight and the TLC (silica gel, 10% MeOH in CH2CI2) showed complete disappearance of the starting alcohol. The reaction mixture was diluted with CH2CI2 (40 mL) and washed with saturated NaHC03 (50 mL), water (60 mL) and brine (60 mL). The combined organic layers were dried over anhyd. Na2SC"4 and solvents were removed in vacuo. The crude product thus obtained was purified by Combiflash Rf purification system (40 g silicagel, 0-10 % MeOH in CH2CI2) to isolate the pure product (0.062 g, 62%) as a colorless oil. 1H NMR (400 MHz, CDC13) δ 5.74 - 5.58 (m, 2H), 5.51 (dtt, J = 9.7, 6.8, 1.3 Hz, 2H), 4.95 - 4.75 (m, 1H), 4.61 (d, J = 6.8 Hz, 4H), 2.35 - 2.24 (m, 8H), 2.22 (d, J = 7.9 Hz, 6H), 2.09 (q, J = 6.9 Hz, 4H), 1.83 - 1.72 (m, 2H), 1.60 (dd, J = 14.4, 7.2 Hz, 4H), 1.49 (d, J = 5.7 Hz, 4H), 1.41 - 1.13 (m, 30H), 0.88 (t, J = 6.9 Hz, 6H). 13C NMR (101 MHz, CDC13) δ 173.72, 173.36, 135.40, 123.35, 74.12, 60.18, 58.95, 45.46, 34.30, 34.11, 32.45, 31.67, 29.38, 29.35, 29.17, 29.07, 28.84, 27.53, 25.28, 24.93, 23.16, 22.59, 14.06. MW calc. for C41H75NO6 (MH+): 678.04, found: 678.5.
Example 18
The following shorter route was used for the synthesis of analogs of Compound 1 of the present invention The commercial 9-bromonon-l-ene 248 was treated with magnesium to form the corresponding Grignard reagent which was reacted with ethylformate to give the corresponding adduct 249 which on treatment with bromobutyryl chloride to provide the bromoester 250. The bromoester 250 on treatment with Ru04 provided the diacid 251. The bromodiacid 251 on treatment with dimethylamine provided the amino diacid 252. The diacid 252 on treatment with oxalyl chloride in the presence of DMF provided the diacid chlorides 253. The lipids 254a-n were synthesized by treating the acid Chloride 253 with respective alcohols. Scheme 18
Figure imgf000159_0001
Figure imgf000159_0002
Figure imgf000161_0001
- 160-
Figure imgf000162_0001
Figure imgf000163_0001
- 162-
Figure imgf000164_0001
Synthesis of nonadeca-l,18-dien-10-ol (249)
To a flame dried 500 mL RB flask, freshly activated Mg turnings (9 g) were added and the flask was equipped with a magnetic stir bar, an addition funnel and a reflux condenser. This set-up was degassed and flushed with argon and 100 mL of anhydrous ether was added to the flask via syringe. The bromide 3 (51.3 g, 250 mmol) was dissolved in anhydrous ether (100 mL) and added to the addition funnel. About 5 mL of this ether solution was added to the Mg turnings while stirring vigorously. An exothermic reaction was noticed (to confirm/accelerate the Grignard reagent formation, 5 mg of iodine was added and immediate decolorization was observed confirming the formation of the Grignard reagent) and the ether started refluxing. The rest of the solution of the bromide was added dropwise while keeping the reaction under gentle reflux by cooling the flask in water. After the completion of the addition the reaction mixture was kept at 35 °C for 1 hour and then cooled in ice bath. Ethyl formate (9 g, 121 mmol) was dissolved in anhydrous ether (100 mL) and transferred to the addition funnel and added dropwise to the reaction mixture with stirring. An exothermic reaction was observed and the reaction mixture started refluxing. After the initiation of the reaction the rest of the ethereal solution of formate was quickly added as a stream and the reaction mixture was stirred for a further period of 1 h at ambient temperature. The reaction was quenched by adding 10 mL of acetone dropwise followed by ice cold water (60 mL). The reaction mixture was treated with aq. H2S04 (10 % by volume, 300 mL) until the solution became homogeneous and the layers were separated. The aq. phase was extracted with ether (2x200 mL). The combined ether layers were dried (Na2S04) and concentrated to afford the crude product which was purified by column (silica gel, 0-10% ether in hexanes) chromatography. The product fractions were evaporated to provide the pure product 249 as a white solid (30.6 g, 90%). 1H NMR (400 MHz, CDC13) δ 7.26 (s, 1H), 5.81 (ddt, J = 16.9, 10.2, 6.7 Hz, 8H), 5.04 - 4.88 (m, 16H), 3.57 (dd, J = 7.6, 3.3 Hz, 4H), 2.04 (q, J = 6.9 Hz, 16H), 1.59 (s, 1H), 1.45 (d, J = 7.5 Hz, 8H), 1.43 - 1.12 (m, 94H), 0.88 (t, J = 6.8 Hz, 2H). 13C NMR (101 MHz, cdcl3) δ 139.40, 114.33, 77.54, 77.22, 76.90, 72.21, 37.70, 34.00, 29.86, 29.67, 29.29, 29.12, 25.85.
Synthesis of nonadeca-l,18-dien-10-yl 4-bromobutanoate (250)
To a solution of the alcohol 249 (5.6 g, 20 mol) in anhydrous DCM (300 mL) was added slowly and carefully Bromobutryl chloride (20 mmol) at 0° C under inert atmosphere. The reaction mixture was warmed to room temperature, stirred for 20 h and monitored by TLC (silica gel, 10% ethyl acetate in hexanes). Upon completion of the reaction, mixture was diluted with water (400 mL) and organic layer was separated out. Organic phase was then washed with sat. solution of NaHC03 (1 x 400 mL) followed by brine (1 x 100 mL) and concentrated under vacuum. Crude product was then purified by silica gel (100-200mesh) column, eluted with 2-3% ethyl acetate in hexane solution to give 6 g (90%) of desired product 250 as colorless liquid. 1H NMR (400 MHz, CDC13) δ 5.80 (ddt, J = 16.9, 10.2, 6.7 Hz, 2H), 5.05 - 4.81 (m, 5H), 3.46 (t, J = 6.5 Hz, 2H), 2.48 (t, J = 7.2 Hz, 2H), 2.17 (p, J = 6.8 Hz, 2H), 2.11 - 1.93 (m, 4H), 1.65 - 1.44 (m, 4H), 1.43 - 1.17 (m, 19H). 13C NMR (101 MHz, cdcl3) δ 172.51, 139.37, 114.35, 77.54, 77.23, 76.91, 74.86, 34.31, 33.99, 33.01, 32.96, 29.65, 29.56, 29.24, 29.09, 28.11, 25.52.
Synthesis of 9-((4-bromobutanoyl)oxy)heptadecanedioic acid (251) To a solution of the bromoester 250 (12. lg, 28.2 mmol) in dichloromethane (300 mL) and acetonitrile (300 mL), RuCl3 (1.16 g, 5 mol ) was added and the mixture was cooled to 10 °C and sodium metaperiodate (60 g) in water (400 mL) was added dropwise. It was stirred at 10 °C for 20 hr. The reaction mixture was diluted with water, The layers were separated and to the organic layer, was added saturated brine solution with stirring followed by 3% sodium sulfide solution drop wise for the decolourisation (dark green to pale yellow). The layers were separated, the organic layer was dried over sodium sulfate and evaporated at reduced pressure to afford pure product. MW calcd for C2oH35Br07 467.39; Found 465.4 (M-2H). 1H NMR (400 MHz, DMSO) δ 11.94 (s, 2H), 4.88 - 4.69 (m, 1H), 3.53 (t, J = 6.6 Hz, 2H), 2.43 (t, J = 7.2 Hz, 2H), 2.17 (t, J = 7.4 Hz, 4H), 2.09 - 1.95 (m, 2H), 1.90 (s, 3H), 1.46 (s, 7H), 1.23 (s, 15H).
Synthesis of 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioic acid (252)
The Bromoacid 251 (2 mmol) is dissolved in 2M solution of dimethylamine in THF (20 mL) and to it 1 g of anhudrous K2C03 was added and the mixture was heated in a pressure bottle at 50 °C overnight. The TLC showed the completion of the reaction. The reaction mixture was acidified with acetic acid and diluted with water (100 mL) and extracted with dichloromethane (2 x 60 mL). The combined organic layers were concentrated dried and used as such in the next reaction. MW calcd for C23H43N06 429.59; Found 430.6 (MH)+. 1H NMR (400 MHz, DMSO) δ 11.87 - 11.82 (m, 7H), 5.75 (d, J = 0.7 Hz, 15H), 4.85 - 4.69 (m, 38H), 3.64 - 3.55 (m, 12H), 3.35 - 2.83 (m, 106H), 3.01 - 2.90 (m, 59H), 2.94 (ddd, J = 30.6, 7.7, 4.0 Hz, 63H), 2.90 - 2.73 (m, 9H), 2.70 (s, 221H), 2.57 - 2.46 (m, 91H), 2.44 - 2.30 (m, 76H), 2.17 (t, J = 7.3 Hz, 147H), 1.89 (tq, J = 15.5, 7.6 Hz, 88H), 1.79 - 1.69 (m, 13H), 1.65 - 1.32 (m, 311H), 1.28 (d, J = 46.0 Hz, 598H).
Synthesis of 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioyl chloride (253)
The diacid 252 is converted to the corresponding diacid chloride 253 by treating it with oxalyl chloride in dichloromethane in the presence of catalytic DMF and the crude acid chloride obtained after the concentration of the reaction mixture was used as such for the coupling with different alcohols.
General procedure for the synthesis of cationic lipids 254a-n To a solution of the acid chloride 253 (500 mg, 1 mmol) in dichloromethane (30 mL) the corresponding alcohol (5 equivalent) was added at room temperature followed by solid K2C03 (1 g) and the solution was stirred for 16 h at room temperature. The reaction mixture was diluted with dichloromethane (100 mL) and washed with satd. NaHC03 (100 mL) and the organic layer was dried (Anhyd. Na2S04) and concentrated to obtain the crude product which was purified by Combiflash Rf purification system.
Compound 254b: By using the above procedure the lipid 254b was isolated in 72% yield (554 mg). 1H NMR (400 MHz, CDC13) δ 4.91 - 4.78 (m, 1H), 4.05 (t, J = 6.7 Hz, 4H), 3.81 (s, 6H), 3.63 (t, J = 6.4 Hz, 1H), 2.29 (dt, J = 15.2, 7.5 Hz, 8H), 2.21 (s, 6H), 1.84 - 1.69 (m, 2H), 1.57 (dt, J = 13.4, 5.2 Hz, 9H), 1.53 - 1.40 (m, 4H), 1.27 (s, 43H). 13C NMR (101 MHz, cdcl3) δ 174.45, 174.13, 173.59, 77.54, 77.22, 76.91, 74.34, 64.54, 59.17, 51.65, 45.67, 34.56, 34.35, 34.27, 32.67, 29.59, 29.40, 29.33, 29.31, 29.25, 28.83, 26.06, 25.51, 25.18, 25.11, 23.38. MW calcd for C43H79NO10 770.09; Found 770.68.
Compound 254c: By using the above procedure the lipid 254c was isolated in 69% (490 mg). 1H NMR (400 MHz, CDC13) δ 5.71 - 5.36 (m, 4H), 4.89 - 4.72 (m, 1H), 4.59 (d, J = 6.8 Hz, 4H), 2.26 (ddd, J = 22.3, 13.0, 8.6 Hz, 9H), 2.19 (s, 6H), 2.12 - 1.95 (m, 4H), 1.82 - 1.68 (m, 2H), 1.63 - 1.37 (m, 8H), 1.37 - 1.00 (m, 32H), 0.85 (t, J = 6.8 Hz, 6H). 13C NMR (101 MHz, cdcl3) δ 173.94, 173.57, 135.61, 123.57, 77.54, 77.22, 76.91, 74.34, 60.40, 59.16, 45.65, 34.52, 34.33, 32.66, 31.88, 29.59, 29.57, 29.38, 29.28, 29.06, 27.75, 25.49, 25.14, 23.35, 22.81, 14.28. MW calcd for C43H83N06: 710.12; Found 710.81.
Compound 254d: By using the above procedure the lipid 254d was isolated in 67% yield (456 mg). 1H NMR (400 MHz, CDC13) δ 4.92 - 4.78 (m, 1H), 4.05 (t, J = 6.7 Hz, 4H), 3.63 (t, J = 6.4 Hz, 1H), 2.39 - 2.24 (m, 8H), 2.21 (s, 6H), 1.89 - 1.70 (m, 2H), 1.69 - 1.54 (m, 8H), 1.51 (dd, J = 17.2, 6.3 Hz, 4H), 1.27 (s, 42H), 0.88 (t, J = 6.8 Hz, 6H). MW calcd for: C41H79N06: 682.07; Found 682.96.
Compound 254e: By using the above procedure the lipid 254e was isolated in 70% (474 mg). 1H NMR (400 MHz, CDC13) δ 5.49 (ddd, J = 12.9, 9.8, 7.3 Hz, 2H), 5.40 - 5.23 (m, 2H), 4.92 - 4.77 (m, 1H), 4.05 (t, J = 6.9 Hz, 4H), 2.32 (ddd, J = 23.4, 14.5, 7.1 Hz, 12H), 2.21 (s, 6H), 2.07 - 1.91 (m, 4H), 1.84 - 1.70 (m, 2H), 1.66 - 1.39 (m, 8H), 1.40 - 1.15 (m, 26H), 0.88 (t, J = 6.8 Hz, 5H). MW calc. for C41H75NO6 (MH+): 678.04, found: 678.5.
Compound 254f: By using the above procedure the lipid 254f was isolated in 73% (559 mg). 1H NMR (400 MHz, CDC13) δ 5.87 - 5.62 (m, 2H), 5.55 (dtt, J = 9.1, 6.4, 1.3 Hz, 2H), 4.93 - 4.75 (m, 1H), 4.50 (dd, J = 6.5, 0.6 Hz, 4H), 2.40 - 2.17 (m, 13H), 2.12 - 1.95 (m, 4H), 1.89 - 1.67 (m, 2H), 1.69 - 1.44 (m, 7H), 1.41 - 1.12 (m, 25H), 0.88 (t, J = 6.9 Hz, 5H). MW calc. for C4iH75N06 (MH+): 678.04, found: 678.5.
Compound 254 g: By using the above procedure the lipid 254g was isolated in 63% (432 mg). 1H NMR (400 MHz, CDC13) δ 4.93 - 4.77 (m, 1H), 4.20 - 3.95 (m, 4H), 2.44 - 2.23 (m, 8H), 2.21 (s, 6H), 1.84 - 1.66 (m, 3H), 1.68 - 1.34 (m, 15H), 1.35 - 1.17 (m, 20H), 1.17 - 1.04 (m, 5H), 0.88 (dd, J = 12.4, 6.6 Hz, 16H). MW calcd for C43H83N06: 710.12; Found 710.81.
Compound 254h: By using the above procedure the lipid 254h was isolated in 66% (466 mg). 1H NMR (400 MHz, CDC13) δ 5.08 (ddd, J = 7.1, 5.9, 1.3 Hz, 2H), 4.91 - 4.75 (m, 1H), 4.22 - 3.97 (m, 4H), 2.39 - 2.22 (m, 8H), 2.23 (d, J = 16.7 Hz, 7H), 2.09 - 1.84 (m, 4H), 1.86 - 1.71 (m, 3H), 1.71 - 1.02 (m, 44H), 0.91 (t, J = 4.9 Hz, 6H). MW calcd for C43H79N06: 706.12; Found 706.81.
Example 19
In another approach the following synthetic approach is used for the synthesis of Compound 1 of the present invention.
Scheme 19
1. Ag20/BnBr 1) Mg, MeOCHO
2. Benzyltrifluoroacetamide/
triflic acid (cat)
Figure imgf000169_0001
Example 20
Scheme 20
Bn-Br CBr4
.OBn ^OBn
HO NaH, THF " HO PPh,, DCM
Figure imgf000170_0001
ALNY-319
8-benzyloxy-octan-l-ol (2): To a stirred suspension of NaH (60% in oil, 82 g, 1.7096 mol) in 500mL anhydrous DMF, a solution of compound 1 (250g, 1.7096 mol) in 1.5 L DMF was added slowly with dropping funnel at 0° C. Reaction mixture was stirred for 30 min and to it Benzyl bromide (208.86 mL, 1.7096 mol) was added slowly under nitrogen atmosphere. Reaction was then warmed to ambient temperature and stirred for 10 h. After completion of reaction, mixture was quenched with crushed ice (~2kg) and extracted with Ethyl acetate (2 x 1L). Organic layer washed with water (1L) to remove unwanted DMF, dried over Na2S04 and evaporated to dryness under vacuum. The crude compound was purified on 60-120 silica gel, eluted with 0-5% MeOH in DCM to afford compound 2 (220g, 54%) as pale yellow liquid. H1 NMR (400MHz, CDC13): δ = 7.33-7.24 (m, 5H), 4.49 (s, 2H), 3.63-3.60 (m, 2H), 3.47-3.43 (m, 2H), 1.63-1.51 (m, 4H), 1.39-1.23 (m, 8H).
(8-bromo-octyloxymethyl)-benzene (3): Compound 2 (133g, 0.5635mol) was dissolved in 1.5 L of DCM, CBr4 (280.35g, 0.8456mol) was added into this stirring solution and reaction mixture was cooled to 0°C under inert atmosphere. PPh (251.03g, 0.957 lmol) was then added in portions keeping the temperature below 20°C and after complete addition reaction was stirred for 3 h at room temperature and monitored by TLC. After completion of reaction, solid (PPh30) precipitated out from the reaction mixture was filtered off and filtrate was diluted with crushed ice (~ 1.5kg) and extracted with DCM (3 x 750mL). Organic layer was separated, dried over an. Na2S04 and distilled under vacuum. Resulting crude compound was chromatographed on 60-120 mesh silica gel column using 0-5 % ethyl acetate in hexanes as eluting system to give compound 3 (150g, 89%) as pale yellow liquid. H1 NMR (400MHz, CDC13): δ = 7.33-7.25 (m, 5H), 4.49 (s, 2H), 3.47-3.41 (m, 2H), 3.41-3.37 (m, 2H), 1.86-1.80 (m, 4H), 1.62-1.56(m, 2H), 1.42-1.29 (m, 8H).
1, 17-bis-benzyloxy-heptadecan-9-ol (4): To freshly activated Mg turnings (24.08g, 1.003mol) was added 200mL anhydrous THF was added followed by the addition of pinch of iodine into the mixture under inert atmosphere. After initiation of the Grignard formation a solution of Compound 3 (150g, 0.5016mol) in 1 L of dry THF was added slowly controlling the exothermic reaction. After complete addition reaction was refluxed for lh and then cooled to room temperature. (60.24g, 1.0033mol) methyl formate was then added slowly and reaction was continued for 2h. After completion, the reaction was quenched by slow addition of 10% HCl followed by water (1 L) and extracted with Ethyl Acetate (3 x 1L). Organic layer was taken in 5 lit beaker, diluted with 500mL of methanol and cooled to 0°C. To this solution excess of NaBH4 (~ 5eq) was added in portions to ensure the hydrolysis of formate ester which was not cleaved by addition of HCl. Resulting solution was stirred for an hour and then volatilites were stripped off under vacuum. Residue was taken in water (1 L) and acidified by 10% HCl solution (P 4). Product was then extracted out with ethyl acetate (3 x 1 L). Organic phase was then dried and concentrated on rotary evaporator to get the desired compound 4 (57g, 24%) as solid. H1 NMR (400MHz, CDC13): δ = 7.35-7.32 (m, 8H), 7.29-7.24 (m, 2H), 4.49 (s, 4H), 3.56 (m, 1H), 3.46- 3.43 (m, 4H), 1.63-1.56 (m, 4H), 1.44-1.34 (m, 28H). C13 NMR (100MHz, CDC13): δ = 138.56, 128.21, 127.49, 127.34, 72.72, 71.76, 70.37, 37.37, 29.64, 29.56, 29.47, 29.33, 26.07, 25.54.
[9-benzyloxy-l-(8-benzylozy-octyl)-nonyloxy]-tert-butyl-dimethyl-silane (5): Compound 4 (56 g, 0.1196 mol) was dissolved in 700 mL of anhydrous THF and cooled to 0 °C. TBMS-C1 (36.06g, 0.2396mol) was added slowly followed by addition of Imidazole (32.55 g, 0.4786 mol) under inert atmosphere. Reaction was then stirred at room temperature for 18h. Reaction was judged complete by TLC and then quenched with ice (~lkg) and extracted with Ethyl acetate (3 x 500mL). Organic layer was separated, washed with Sat NaHC03 solution to remove the acidic impurity, dried over Na2S04 and evaporated under reduce pressure to obtain crude compound which was purified by silica gel (60-120 mesh) and eluted with 0- 10% ethyl acetate hexane to yield (60g, 82%) of compound 5 as yellowish oil. H1 NMR (400MHz, CDC13): δ = 7.33-7.24 (m, 10H), 4.49 (s, 4H), 3.60-3.57 (m, 1H), 3.46-3.43 (m, 4H), 1.61-1.54 (m, 4H), 1.41-1.26 (m, 28H), 0.87 (s, 9H), 0.02 (s, 6H)
9-(tert-butyl-dimethyl-silanyloxy)-heptadecane-l, 17-diol (6): Compound 5 (60 g, 0.1030 mol) was dissolved in 500mL ethyl acetate and degassed with N2 for 20 min. (10 wt %) Pd on carbon (12 g) was added and reaction was stirred under H2 atmosphere for 18 h. After completion of reaction (by TLC) mixture was filtered through celite bed and washed with ethyl acetate. Filtrate was evaporated under vacuum. The compound 6 (19 g, 46%) thus obtained was pure enough to carry out the next reaction. H1 NMR (400MHz, CDC13): δ = 3.64-3.58 (m, 5H), 1.59 (br, 2H), 1.57-1.51 (m, 4H), 1.38-1.22 (m, 28H), 0.87 (s, 9H), 0.02 (s, 6H).
9-(tert-butyl-dimethyl-silanyloxy)-heptadecanedioic acid (7): To a stirred solution of 6 (2 g, 0.0049 mol) in anhydrous DMF (40 mL) was added pyridinium dirchromate (2.7 g, 0.0074 mol) at 0 °C under inert atmosphere. Reaction mixture was then allowed to warm to room temperature over a period of 10-15 minutes and continued for 24h. Progress of the reaction was monitored by TLC. After complete oxidation reaction was diluted with water (lOOmL). Aqueous phase was extracted with DCM (3 x 40mL). Organic phase was washed with brine (lx 25mL) and concentrated under vacuum to afford crude acid which was then purified by (100-200 mesh) silica gel column using 0-30% ethyl acetate in hexanes system. Pure product 26-003 was obtained (0.7g, 33%) as pale yellow oil. H1 NMR (400MHz, CDC13): δ = 3.61-3.56 (m, 1H), 2.35-2.32 (m, 4H), 1.64-1.59 (m, 4H), 1.40-1.19 (m, 24H), 0.86 (s, 9H), 0.017 (s, 6H); LC-MS [M+H] - 431.00; HPLC (ELSD) purity - 96.94%
Di((Z)-non-2-en-l-yl) 9-((tert-butyldimethylsilyl)oxy)heptadecanedioate (8): The diacid 7 (0.42 g, 0.97 mmol) was dissolved in 20 mL of dichloromethane and to it ci5,-2-nonen-l-ol (0.35 g, 2.44 mmol) was added followed by Hunig's base (0.68 g, 4.9 mmol) and DMAP (12 mg). To this mixture EDCI (0.47 g, 2.44 mmol) was added and the reaction mixture was stirred at room temperature overnight and the TLC (silica gel, 5% MeOH in CH2CI2) showed complete disappearance of the starting acid. The reaction mixture was diluted with CH2CI2 (40 mL) and washed with saturated NaHC03 (50 mL), water (60 mL) and brine (60 mL). The combined organic layers were dried over anhyd. Na2S04 and solvents were removed in vacuo. The crude product thus obtained was purified by Combiflash Rf purification system (40 g silicagel, 0-10 % MeOH in CH2C12) to isolate the pure product 8 (0.35 g, 53%) as a colorless oil. 1H NMR (400 MHz, CDC13): δ 1H NMR (400 MHz, CDC13) δ 5.64 (dt, J = 10.9, 7.4 Hz, 2H), 5.58 - 5.43 (m, 2H), 4.61 (d, J = 6.8 Hz, 4H), 3.71 - 3.48 (m, 1H), 2.30 (t, J = 7.6 Hz, 4H), 2.20 - 1.98 (m, 4H), 1.71 - 1.53 (m, 4H), 1.31 (ddd, J = 8.3, 7.0, 3.7 Hz, 34H), 1.07 - 0.68 (m, 14H), 0.02 (s, 5H). 13C NMR (101 MHz, CDC13) δ 178.18, 139.81, 127.78, 81.73, 81.42, 81.10, 76.72, 64.59, 41.52, 41.32, 38.76, 36.09, 34.10, 33.93, 33.80, 33.70, 33.59, 33.55, 33.26, 31.95, 30.34, 29.69, 29.58, 29.39, 27.01, 22.56, 18.48, 0.01.
Di((Z)-non-2-en-l-yl) 9-hydroxyheptadecanedioate (9): The silyl protected diester 8 (0.3 g, 0.44 mmol) was dissolved in 1 M solution of TBAF in THF (6 mL) and the solution was kept at 40 °C for two days after which the TLC showed the completion of the reaction. The reaction mixture was diluted with water (60 mL) and extracted with ether (2 x 50 mL). The combined organic layers were concentrated and the thus obtained crude product was purified by column to isolate the pure product (0.097 g, 39%). 1H NMR (400 MHz, CDC13) δ 5.64 (dt, J = 10.9, 7.4 Hz, 2H), 5.52 (dt, J = 11.0, 6.8 Hz, 2H), 4.61 (d, J = 6.8 Hz, 4H), 3.57 (s, 1H), 2.30 (t, J = 7.5 Hz, 4H), 2.09 (q, J = 7.1 Hz, 4H), 1.75 - 1.53 (m, 4H), 1.53 - 1.06 (m, 36H), 0.88 (t, J = 6.8 Hz, 6H). 13C NMR (101 MHz, CDC13) δ 173.98, 135.64, 123.57, 77.54, 77.22, 76.91, 72.14, 60.41, 37.69, 34.54, 31.89, 29.70, 29.60, 29.44, 29.29, 29.07, 27.76, 25.80, 25.15, 22.82, 14.29.
Di((Z)-non-2-en-l-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate: The alcohol 9 (0.083 g, 0.147 mmol) was dissolved in 20 mL of dichloromethane and to it dimethylaminobutyric acid hydrochloride (0.030 g, 0.176 mmol) was added followed by Hunig's base (0.045 g, 0.44 mmol) and DMAP (2 mg). To this mixture EDCI (0.034 g, 0.176 mmol) was added and the reaction mixture was stirred at room temperature overnight and the TLC (silica gel, 10% MeOH in CH2CI2) showed complete disappearance of the starting alcohol. The reaction mixture was diluted with CH2CI2 (40 mL) and washed with saturated NaHC03 (50 mL), water (60 mL) and brine (60 mL). The combined organic layers were dried over anhyd. Na2S04 and solvents were removed in vacuo. The crude product thus obtained was purified by Combiflash Rf purification system (40 g silicagel, 0-10 % MeOH in CH2CI2) to isolate the pure product (0.062 g, 62%) as a colorless oil. 1H NMR (400 MHz, CDC13) δ 5.74 - 5.58 (m, 2H), 5.51 (dtt, J = 9.7, 6.8, 1.3 Hz, 2H), 4.95 - 4.75 (m, 1H), 4.61 (d, J = 6.8 Hz, 4H), 2.35 - 2.24 (m, 8H), 2.22 (d, J = 7.9 Hz, 6H), 2.09 (q, J = 6.9 Hz, 4H), 1.83 - 1.72 (m, 2H), 1.60 (dd, J = 14.4, 7.2 Hz, 4H), 1.49 (d, J = 5.7 Hz, 4H), 1.41 - 1.13 (m, 30H), 0.88 (t, J = 6.9 Hz, 6H). 13C NMR (101 MHz, CDC13) δ 173.72, 173.36, 135.40, 123.35, 74.12, 60.18, 58.95, 45.46, 34.30, 34.11, 32.45, 31.67, 29.38, 29.35, 29.17, 29.07, 28.84, 27.53, 25.28, 24.93, 23.16, 22.59, 14.06. MW calc. for C41H75N06 (MH+): 678.04, found: 678.5.
In another embodiment the following shorter route was used for the synthesis of the di((Z)-non- 2-en-l-yl) 9-((4-(dimethylamino)butanoyl)oxy)heptadecanedioate. The commercial 9- bromonon-l-ene 10 was treated with magnesium to form the corresponding Grignard reagent which was reacted with ethylformate to give the corresponding adduct 11 which on treatment with bromobutyryl chloride to provide the bromoester 12. The bromoester 12 ontreatment with Ru04 provided the diacid 13. The bromodiacid 13 on treatment with dimethylamine provided the amino diacid 14. The aminodiacid 14 on coupling with the alcohol 15 provided the product in good yields. Example 21
Scheme 21
Figure imgf000175_0001
r c ac cat)
Figure imgf000175_0002
ALNY-319
Example 22
Scheme 22
I OH
Figure imgf000176_0001
Example 23
Scheme 23
Figure imgf000177_0001
HORx, EDCI, DIPEA, DMAP
Figure imgf000177_0002
Example 24 Scheme 24
Figure imgf000178_0001
Compound 501: To a stirred solution of 2-hydroxy 1-octanol 5g (31.25 mmol), DMAP 0.38g (3.1 mmol) in dry pyridine (100 mL) was added DMTr-Cl and stirred at room temperature for 14 h. 10 mL of water was added and extracted with ethyl acetate, washed with saturated NaHC03 and brine. The organic layer was dried over Na2S04 and concentration of the solvent gave 20g of crude product 500 which was co-evaporated with toluene twice and used for the next step without further purification. To the above crude DMTr ether in dry THF (250 mL) were added NaH and iodo methane at 0°C and then brought to room temperature over 30 min. and then stirred for two days. 5 mL of water was added and concentrated followed by column chromatography (0-30 % ethyl acetate in hexane) gave the corresponding product 501 (10.25 g, Rf: 0.45, 20 % ethyl acetate in hexane) and 8.4 g of recovered starting material 500. 1H NMR (400 MHz, CDC13) δ 7.47-6.8 (m, 13 H), 3.79 (s, 6 H), 3.42 (s, 3 H), 3.29-3.26 (m, 1H), 3.13- 3.04 (m, 2 H), 1.55-1.47 (m, 2 H), 1.3-1.2 (m, 10 H), 0.89 (t, J = 6.4 Hz, 3 H).
Alcohol 502: The compound 501 (10.25 g, 21.5 mmol) was dissolved in 75 mL of 80 % acetic acid and stirred at room temperature for 14 h. 10 mL of methanol was added and concentrated, followed by column chromatography (0-50 % ethyl acetate in hexane) yielded the expected product 502 as colorless oil (1.8 g, 82 , Rf: 0.3, 30 % ethyl acetate in hexane). 1H NMR (400 MHz, CDCI3) δ 3.71-3.65 (m, 1 H), 3.5-3.45 (m, 1 H), 3.41 (s, 3 H), 3.28-3.25 (m, 1 H), 1.93-1.9 (m, 1 H), 1.45-1.41 (m, 2 H), 1.39-1.27 (m, 10 H), 0.88 (s, J = 6.8 Hz, 3 H).
Compound 503: Compound 503 was synthesized following general experimental procedure for compound 213. 0.3g as pale yellow oil (52 , Rf = 0.2, 5 % methanol in dichloromethane). 1H NMR (400 MHz, CDC13) δ 4.87-4.84 (m, 1 H), 4.18-4.00 ( m, 4 H), 3.4 (s, 6 H), 3.37-3.19 (m, 2 H), 2.34-2.26 (m, 6 H), 2.2 (s, 6 H), 1.8-1.6 (m, 2 H), 1.63-1.2 (m, 50 H), 0.88 (s, J = 6.8 Hz, 6 H).
Example 25 Scheme 25
Figure imgf000179_0001
167 mg, 66 % (2 steps)
Compound 504: To a stirred solution of alcohol 11 (4.01 g, 22.25 mmol), TBDPS-C1 (12.24 g, 44.5 mmol) and DMAP (0.54 g, 4.42 mmol) was added triethyl amine (8.99 g, 90 mmol) and stirred at room temper for 14 h. To the above solution was added imidazole (1.51 g, 22.25 mmol) and continued to stir for 14 h at room temperature. 20 mL of water was added and extracted with DCM followed by washing with 2N HCl, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0- 10 % ethyl acetate in hexane) to yield compound 504 (7.38 g, 79 %, Rf. 0.8, 5 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 7.68-7.66 (m, 4 H), 7.43-7.33 (m, 6 H), 5.86-5.76 (m, 2 H), 5.02-4.91 (m, 4 H), 3.73-3.67 (m, 1 H), 2.04- 1.99 (m, 4H), 1.42-1.08 (m, 24 H), 1.05 (s, 9 H).
Compound 505: To a stirred solution of diene 504 (7.38 g, 17.6 mmol) and RuCl3 (0.18g, 0.88 mmol) in 400 mL of DCM/CH3CN(1 : 1) was added NaI04 (37.6 g, 176 mmol) dissolved in 400 mL of water drop wise around 5° C over 30 min. and stirred at room temperature for 3 h. The organic layer was separated followed by washing with 3 % Na2S solution (100 mL), water (250 mL) brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product 505 (4 g, 42 , Rf: 0.3, 40 % ethyl acetate in hexane), which was used for the next step without further purification.
Compound 506: To a stirred solution of the acid 505 (4 g, 7.22 mmol), HBTU (6.02 g, 15.88 mmol), HOBt (2.14 g, 15.88 mmol) and DMAP (88 mg, 0.72 mmol) in 75 mL of dry DCM was added 5 mL of methanol and stirred at room temperature for 14 h. 10 mL of water was added followed by extraction with DCM (3 x 50 mL), washing with saturated NaHC03, water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0-30 % ethyl acetate in hexane) to yield compound 506 (2 g, 47.6 , Rf: 0.3, 10 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 7.67-7.65 (m, 4 H), 7.41-7.33 (m, 6 H), 3.70-3.64 (m, 1 H), 3.66 (s, 6 H), 2.28 (t, J = 7.2 Hz, 4 H), 1.63- 1.07 (m, 24H), 1.04 (s, 9 H).
Compound 507: To a stirred solution of dimethyl ester 506 (1.0 g, 1.79 mmol) in dry THF (20 mL) were added KHMDS (0.752 g, 3.76 mmol) and methyl iodide (0.762 g, 5.37 mmol) at 0°C and then brought to room temperature over 30 min. and stirred for 24 h. 10 mL of sat. NH4C1 solution was added followed by extraction with ethyl acetate (3 x 50 mL), washing with water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product, which was purified by column chromatography (0-5 % ethyl acetate in hexane) to obtain the product 507 (0.218g, 20 , Rf: 0.8, 5 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 7.68-7.65 (m, 4 H), 7.41-7.33 (m, 6 H), 3.70-3.67 (m, 1 H), 3.67 (s, 6 H), 2.43-2.38 (m, 2 H), 1.59-1.07 (m, 24 H), 1.13 (d, J = 7.2 Hz, 6 H), 1.04 (s, 9 H).
Compound 509: To a stirred solution of methyl ester 507 (0.4 g, 0.66 mmol) in 10 mL of MeOH/THF (1: 1) was added LiOH (0.079 g, 3.27 mmol) in 1 mL of water and stirred at room temperature for 24 h. To the above solution was added KOH (0.183 g, 3.27 mmol) in 1 mL of water and stirred for another 2 days. 2 mL of sat. NH4C1 solution was added followed by extraction with ethyl acetate (3 x 25 mL), washing with water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product 508 (0.45 g, Rf: 0.2, 10 % ethyl acetate in hexane), which was used for the next step without further purification. To a stirred solution of the above di-acid 508 (0.45 g), cw-2-Nonen-l-ol (0.66 g, 4.6 mmol) and EDC-HCl (0.82 g, 4.6 mmol) in dry DCM (15 mL) was added DIEA (1.2 g, 9.24 mmol) and stirred at room temperature for 3 days. 10 mL of water was added followed by extraction with DCM followed by washing with 2N HC1, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0-10 % ethyl acetate in hexane) to yield compound 509 (0.3 g, 55 , Rf: 0.5, 3 % ethyl acetate in hexane). 1H NMR (400 MHz, CDCI3) δ 7.67-7.65 (m, 4 H), 7.42-7.33 (m, 6 H), 5.67-5.6 (m, 2 H), 5.55-5.49 (m, 2 H), 4.615 (d, J = 4 Hz, 4 H), 3.71-3.65 (m, 1 H), 2.44-2.35 (m, 2 H), 2.10 (q, J = 8.0 Hz, 4 H), 1.64- 1.07 (m, 40 H), 1.13 (d, J = 8.0 Hz, 6 H), 1.04 (s, 9 H), 0.86 (t, J = 10 Hz, 6 H).
Compound 511: To a stirred solution of silyl ether 509 (0.3 g, 0.36 mmol) in dry THF were added pyridine (1 mL) and HF'Pyr., (1 mL) drop wise and stirred at 45 C for 48 h. The solvent was evaporated and used for the next step without purification.
To a stirred solution of the above crude alcohol 510, /V,/V-Dimethyl amino butyric acid (0.34 g, 2.04 mmol), EDC'HCl (0.39 g, 2.04 mmol) and DMAP (0.06 g, 0.51 mmol) in dry DCM (10 mL) was added DIEA (0.5 g, 3.88 mmol) and stirred at room temperature for 2 days. 10 mL of water was added followed by extraction with DCM (3 x 25 mL), washing with saturated NaHC03, water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0-30 % ethyl acetate in 1 % TEA containing hexane) to yield compound 511 (0.167 g, 66 %, Rf: 0.4, 10 % MeOH in DCM).
Molecular weight for C43H79N06 (M+H)+ Calc. 706.59, Found 706.5.
Example 26 Scheme 26
Figure imgf000182_0001
Compound 512: To a stirred solution of 4-Pentynoic acid in 100 mL of THF/HMPA (4: 1) at - 78 C was added nBuLi (3.1 g, 49 mmol) drop wise and stirred for 30 min. Then the reaction mixture was brought to 0°C and stirred for 2 h. Again, the reaction mixture was cooled to -78 C and n-butyl bromide (3.07 g, 22.44 mmol) was added drop wise and stirred at room temperature for 14 h. 10 mL of sat. NH4C1 solution was added followed by extraction with ethyl acetate (3 x 25 mL), washing with water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product , which was purified by column chromatography (0-30 % ethyl acetate in hexane) to yield compound 512 (0.4 g, Rf. 0.8, 30 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 2.59-2.55 (m, 2 H), 2.49-2.44 (m, 2 H), 2.16-2.11 (m, 2 H), 1.49-1.34 (m, 4 H), 0.9 (t, J = 6.0 Hz, 3 H).
Compound 513: To a suspension of Ni(OAc)2 (0.45 g, 2.53 mmol) in EtOH (20 mL) was added NaBH4 (0.096 g, 12.65 mmol) portion wise at room temperature and stirred for 15 min. under H2 atm. Filtered off the solid followed by concentration of the solvent gave compound 513 ( 0.35 g, 88.6 , Rf: 0.6, 20 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 10.88 (br s, IH), 5.47-5.41 (m, IH), 5.35-5.31 (m, IH), 2.43-2.33 (m, 4 H), 2.07-2.03 (m, 2 H), 1.36-2.27 (m, 4 H), 0.9 (t, J = 8.0 Hz, 3 H). Compound 515: To a stirred solution of di-acetate 514 (1.5 g, 3.09 mmol) in MeOH (100 mL) was added a piece of sodium metal (0.05 g, 2.17 mmol) and stirred at room temperature for 14 h. Neutralized with dry ice and concentrated followed by extraction with ethyl acetate (3 x 50 mL), washing with water, dried over anhydrous Na2S04. Concentration of the solvent gave the crude product 515 (1.1 g, 88.7 %) , which was used for the next step without purification.
Compound 516: To a stirred solution of the above diol 515 (0.4 g, 1 mmol), 513 (0.341 g, 2.19 mmol), DMAP (0.1 g, 0.82 mmol) and EDC'HCl (0.57 g, 2.98 mmol) in dry DCM (15 mL) was added DIEA (5.97 g, 6 mmol) and stirred at room temperature for 2 days. 10 mL of water was added followed by extraction with ethyl acetate followed by washing with IN HC1, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0-10 % ethyl acetate in hexane) to yield compound 516 (0.335 g, 50 , Rf: 0.6, 5 % ethyl acetate in hexane).1H NMR (400 MHz, CDC13) δ 5.45-5.38 (m, 2H), 5.36-5.29 (m, 2H), 4.06 (t, J = 8 Hz, 4 H), 3.63-3.58 9m, 1 H), 2.39-2.31 (m, 8 H), 2.07- 2.02 (m, 4 H), 1.65-1.57 (m, 4 H), 1.4-1.28 (m, 32 H), 0.9 (t, J = 6.0 Hz, 6 H), 0.88 (s, 9 H), 0.03 (s, 6 H).
Compound 517: To a stirred solution of silyl ether 516 (0.3 g, 0.36 mmol) in dry THF (5 mL) were added pyridine (1 mL) and HF'Pyr. (1 mL) drop wise and stirred at 45 C for 24 h. The solvent was evaporated followed by purification by column chromatography gave product 517 (0.2 g, 72 , Rf: 0.4, 10 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 5.43-5.36 (m, 2H), 5.34-5.27 (m, 2H), 4.04 (t, J = 8 Hz, 4 H), 3.59-3.53 (m, 1 H), 2.37-2.3 (m, 8 H), 2.05-2.0 (m, 4 H), 1.61-1.29 (m, 37 H), 0.88 (t, J = 8.0 Hz, 6 H).
Compound 518: To a stirred solution of the alcohol 517 (0.2 g, 0.355 mmol), N,N-Dimethyl amino butyric acid (0.36 g, 2.14 mmol), EDC'HCl (0.406 g, 2.14 mmol) and DMAP (0.043 g, 0.36 mmol) in dry DCM (10 mL) was added DIEA (0.55 g, 4.26 mmol) and stirred at room temperature for 2 days. 10 mL of water was added followed by extraction with DCM (3 x 25 mL), washing with saturated NaHC03, water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0-30 % ethyl acetate in 1 % TEA containg hexane) to yield compound 518 (0.172 g, 72 %, Rf: 0.2, 5 % MeOH in DCM). 1H NMR (400 MHz, CDC13) δ 5.43-5.36 (m, 2H), 5.32-5.27 (m, 2H), 4.87-4.83 (m, 1 H), 4.03 (t, J = 6 Hz, 4 H), 2.36-2.2 (m, 6 H), 2.32 (s, 6 H), 2.03-1.25 (m, 40 H), 0.88 (t, J = 6.0 Hz, 6 H).
Example 27 Scheme 27
Figure imgf000184_0001
Compound 521: To a suspension of Mg in Et20 was added alkyl bromide (25 g, 107.7 mmol) drop wise at 40° C over one hour. Ethyl formate was added to the above reaction mixture at 0-5° C and then the reaction mixture was stirred at room temperature for 14 h. The reaction mixture was poured onto the ice cold sat. NH4C1 solution followed by extraction with Et20 (3 x 250 mL), washing with water, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product, which was re-dissoled in MeOH (250 mL) and a small piece of sodium (0.1 g) was added and stirred at room temperature for 14 h. The solvent was evaporated and 100 mL of water was added followed by filtration of the solid, washing with water (2 x 100 mL) gave pale yellow powder 521 (17 g, 94 %, %, Rf: 0.8, 10 % ethyl acetate in hexane). 1H NMR (400 MHz, CDC13) δ 5.84-5.74 (m, 2H), 5.0-4.89 (m, 4H), 3.64-3.49 (m, 1 H), 2.04- 1.99 (m, 4 H), 1.79 (br s, 1 H), 1.44-1.23 (m, 32 H).
Compound 522: To a stirred solution of 521 (10 g, 29.73 mmol) and DMAP (0.1 g, 0.82 mmol) in dry DCM (50 mL) was added 4-bromo butyryl chloride (6.56 g, 35.68 mmol) and stirred at room temperature for 14 h. 5 mL of saturated NaHC03 was added and the organic layer was separated and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product which was purified by column chromatography (0- 10 % ethyl acetate in hexane) to yield compound 522 (9.6 g, 66.7 , Rf: 0.9, 5 % ethyl acetate in hexane).
Compound 524: Oxidation was carried out to get compound 523 (8.6 g, 83.5 %, Rf. 0.1, 5 % MeOH in DCM) following same experimental procedure as for compound 505. This crude material was dissolved in 2N N,N-dimethyl amine in THF (20 mL) and heated to 60° C in a sealed tube for 14 h. Concentrated the reaction mixture and then pH of the reaction mixture was brought to 3. This mixture was freeze-dried to obtain compound 524 as HC1 salt (4 g, 82 %). Molecular weight for C27H51N06 (M+H)+ Calc. 486.37, Found 486.2. 1H NMR (400 MHz, CDC13) δ 4.94-4.89 (m, 1 H), 3.32-3.3 (m, 2 H), 3.2-3.16 (m, 2 H), 2.91 (s, 6 H), 2.47 (t, J = 8 Hz, 2 H), 2.28 (t, J = 8 Hz, 4 H), 2.05-1.97 (m, 2 H), 1.61- 1.56 (8 H), 1.4- 1.25 (m, 22 H).
Figure imgf000185_0001
Figure imgf000186_0001
Synthesis of ester 525, 526, 527 and 528:
The title compounds were synthesized following the experimental procedure as for compound 516.
Compound 525: (0.75 g, 60 %, Rf: 0.3, 5 % MeOH in DCM). 1H NMR (400 MHz, CDC13) δ 5.65-5.59 (m, 2 H), 5.53-5.47 (m, 2 H), 4.87-4.81 (m, 1 H), 4.595 (d, J = 4.0 Hz, 4 H), 2.43-2.25 (m, 8 H), 2.2 (s, 6H), 2.1-2.03 (m, 4 H), 1.81-1.73 (m, 2 H), 1.61-1.56 (m, 4 H), 1.48-1.47 (m, 4 H), 1.36-1.23 (m, 32 H), 0.86 (t, J = 8.0 Hz, 6 H).
Compound 526: (0.358 g, 60.9 , Rf: 0.5, 5 % MeOH in DCM). 1H NMR (400 MHz, CDC13) δ 4.87-4.81 (m, 1 H), 4.07-3.95 (m, 4 H), 2.32-2.24 (m, 6 H), 2.2 (s, 6H), 1.80-1.69 (m, 4 H), 1.6- 1.14 (m, 46 H), 0.88-0.84 (m, 24 H).
Compound 527: (0.258 g, 56.8 , Rf: 0.5, 5 % MeOH in DCM). Molecular weight for C47H91N06 (M+H)+ Calc. 766.23; Found: 766.7. 1H NMR (400 MHz, CDC13) δ 4.86-4.80 (m, 1 H), 4.12-4.02 (m, 4 H), 2.31-2.23 (m, 8 H), 2.19 (s, 6H), 1.80-1.72 (m, 2 H), 1.66-1.06 (m, 52 H), 0.87 (d, J = 8.0 Hz, 6 H), 0.84 (d, J = 8.0 Hz, 12 H).
Compound 528: (0.3 g, 68.1 , Rf: 0.5, 5 % MeOH in DCM). Molecular weight for C47H91N06 (M+H)+ Calc. 766.23; Found: 766.7. 1H NMR (400 MHz, CDC13) δ 4.86-4.80 (m, 1 H), 4.12-4.02 (m, 4 H), 2.31-2.21 (m, 8 H), 2.19 (s, 6H), 1.79-1.72 (m, 2 H), 1.66-0.98 (m, 52 H), 0.87 (d, J = 8.0 Hz, 6 H), 0.835 (d, J = 4.0 Hz, 12 H). Example 28
Scheme 28:
1. nBuLi
Figure imgf000187_0001
R' = H (529), Propyl (530) R' = H
534: R = Me
X = O or S R' = Propyl
535: R = Propyl
R' = H
536: R = Propyl R' = Propyl
Figure imgf000187_0002
537: R = Me
R' = H
538: R = Me
R' = Propyl
539: R = Propyl
R' = H
540: R = Propyl
R' = Propyl
Synthesis of compounds 533, 534, 535 and 536: The title compounds (1 mmol) are synthesized following the experimental procedure of compound 513 except de-silylation step and it is done using TBAF in THF at room temperature.
Synthesis of compounds 537, 538, 539 and 540: The title compounds (1 mmol) are synthesized following the experimental procedure of compound 525.
Example 29
Scheme 29
ryl
H
Figure imgf000188_0001
242 X = 0/NH
R = alkyl/aryl
n = 0-10
Figure imgf000188_0002
243 X = 0/NH
R = alkyl/aryl
n = 0-10
Compound 243 (X = O/NH, R = alkyl/aryl) can be synthesized as shown in Scheme 16-2. Tosyl group of 239 can be replaced with phthalimide group by nucleophilic substitution. After deprotection followed by coupling with 111 under acidic conditions, 242 can be synthesized. Standard esterification gives cationic lipid 243 and its analogs.
Example 30: Synthesis of ester-containing lipids
Figure imgf000189_0001
Figure imgf000189_0002
24:
Compound 15: Compound 13 (503 mg, 1.0 mmol) was treated with 14 (469 mg, 3.0 mmol) in the presence of EDCI (2.30 g, 12.0 mmol), DMAP (235 mg, 1.92 mmol) and DIEA (8.34 mL, 47.9 mmol) in CH2C12 (50 mL) for 14 h. Aqueous work-up then column chromatography gave compound 15 (1.22 g, 1.54 mmol, 40%).
Molecular weight for C49H92NO6 (M+H)+ Calc. 790.6925, Found 790.7. Compound 16: This compound was synthesized from 13 and tetrahydrolavandulol using a procedure analogous to that described for compound 15. Yield: 0.358 g, 61 %. lH NMR (400 MHz, CDC13) δ 4.87-4.81 (m, 1 H), 4.07-3.95 (m, 4 H), 2.32-2.24 (m, 6 H), 2.2 (s, 6H), 1.80- 1.69 (m, 4 H), 1.6-1.14 (m, 46 H), 0.88-0.84 (m, 24 H).
Compound 17: This compound was synthesized from 12 (1.0 g, 2.15 mmol) and 3 (1.03 g, 5.16 mmol) using a procedure analogous to that described for compound 15.
Yield: 856 mg (50%). 1H NMR (400 MHz, CDC13) δ 4.91 - 4.79 (m, 1 H), 4.08 (t, J = 7.1 Hz, 4 H), 2.35 - 2.25 (m, 14 H), 1.89 - 1.76 (m, 2 H), 1.67 - 1.13 (m, 62 H), 0.88 (t, J = 7.0 Hz, 12 H). 13C NMR (100 MHz, CDC13) δ 174.08, 74.45, 63.08, 45.27, 34.76, 34.56, 34.28, 33.70, 32.61, 32.39, 29.54, 29.36, 29.28, 26.36, 25.47, 25.13, 22.83, 14.26. Molecular weight for C49H96NO6 (M+H)+ Calc. 794.7238, Found 794.6.
Compound 18: This compound was synthesized from 13 (1.0 g, 2.15 mmol) and 3 (1 g) using a procedure analogous to that described for compound 15.
Yield: 1 g (59%). 1H NMR (400 MHz, CDC13) δ 4.94 - 4.74 (m, 1H), 4.17 - 3.85 (m, 4H), 2.46 - 2.19 (m, 12H), 1.93 - 1.79 (m, 2H), 1.74 - 1.45 (m, 10H), 1.37 (d, / = 20.2 Hz, 2H), 1.35 - 1.13 (m, 44H), 0.88 (t, / = 6.9 Hz, 12H). 13C NMR (101 MHz, CDC13) δ 174.19, 77.53, 77.21, 76.90, 63.12, 34.81, 34.66, 34.35, 33.76, 32.66, 32.45, 29.76, 29.73, 29.63, 29.48, 29.39, 26.42, 25.57, 25.23, 22.89, 14.32. Molecular weight for C53H103NO6 (M+H)+ Calc. 850.38, Found 850.7.
Compound 19: This compound was synthesized from 12 and 11 using a procedure analogous to that described for compound 15.
Yield: 860 mg (51%). 1H NMR (400 MHz, CDC13) δ 4.90 - 4.81 (m, 1 H), 4.04 (t, J = 6.8 Hz, 4 H), 2.37 - 2.17 (m, 14 H), 1.84 - 1.06 (m, 48 H), 0.93 - 0.78 (m, 24 H). 13C NMR (100 MHz, CDCI3) δ 174.06, 74.35, 65.51, 64.91, 59.05, 45.51, 43.77, 37.10, 34.55, 34.29, 32.55, 29.54, 29.37, 29.34, 29.28, 28.58, 28.19, 26.99, 26.74, 25.47, 25.15, 22.90, 22.82, 19.60, 19.41, 19.28. Molecular weight for C47H92NO6 (M+H)+ Calc. 766.6925, Found 766.5. Compound 20: This compound was synthesized from 13 and 11 using a procedure analogous to that described for compound 15.
1H NMR (400 MHz, CDC13) δ 4.86 (p, J = 6.2 Hz, 1 H), 4.04 (t, J = 6.7 Hz, 4 H), 2.38 - 2.17 (m, 14 H), 1.84 - 1.07 (m, 56 H), 0.93 - 0.76 (m, 24 H). 13C NMR (100 MHz, CDC13) δ 174.11, 173.46, 74.44, 64.90, 59.06, 45.51, 43.77, 37.11, 34.59, 34.32, 32.57, 29.71, 29.67, 29.57, 29.43, 29.34, 28.58, 28.20, 27.00, 26.75, 25.51, 25.20, 22.90, 22.82, 19.41, 19.28. Molecular weight for C5iH10oN06 (M+H)+ Calc. 822.7551, Found 822.6.
Compound 21: This compound was synthesized from 12 and 6 using a procedure analogous to that described for compound 15.
1H NMR (400 MHz, CDC13) δ 4.91 - 4.78 (m, 1 H), 4.15 - 3.98 (m, 4 H), 2.39 - 2.18 (m, 14 H), 1.84 - 1.11 (m, 44 H), 0.92 - 0.77 (m, 24 H). 13C NMR (100 MHz, CDC13) δ 174.06, 173.44, 74.36, 63.73, 59.03, 45.48, 41.00, 36.98, 34.56, 34.29, 32.54, 29.60, 29.54, 29.49, 29.36, 29.28, 28.52, 25.47, 25.13, 23.15, 22.85, 22.81, 19.49, 18.89. Molecular weight for C45H88N06 (M+H)+ Calc. 738.6612, Found 738.6.
Compound 22: This compound was synthesized from 13 and 6 using a procedure analogous to that described for compound 15.
Yield: 900 mg (57%). 1H NMR (400 MHz, CDC13) δ 4.92 - 4.78 (m, 1H), 4.15 - 3.91 (m, 4H), 3.33 - 3.08 (m, 1H), 2.36 - 2.15 (m, 14H), 1.79 (dq, / = 14.3, 7.2 Hz, 2H), 1.74 - 1.55 (m, 8H), 1.55 - 1.37 (m, 9H), 1.35 - 0.95 (m, 36H), 0.96 - 0.61 (m, 27H). 13C NMR (101 MHzCDCl3) δ 174.16, 173.52, 77.54, 77.22, 76.91, 74.48, 63.76, 59.10, 45.55, 42.02, 41.04, 38.75, 37.09, 37.02, 34.65, 34.36, 32.62, 30.71, 29.75, 29.72, 29.64, 29.62, 29.53, 29.48, 29.44, 29.38, 28.56, 28.45, 25.56, 25.23, 23.59, 23.23, 22.90, 22.86, 19.54, 19.03, 18.94. Molecular weight for C49H95N06 (M+H)+ Calc. 794.2817, Found 794.7.
Compound 24: This compound was synthesized from 13 and 23 using a procedure analogous to that described for compound 15.
Yield: 0.567 g (30 %). 1H NMR (400 MHz, CDC13) δ 4.85 (p, / = 6.1 Hz, 1H), 4.20 - 3.93 (m, 4H), 2.41 - 2.18 (m, 13H), 1.92 - 1.72 (m, 2H), 1.56 (ddd, / = 27.4, 16.4, 5.8 Hz, 12H), 1.39 (s, 2H), 1.25 (s, 54H), 0.91 (dt, / = 13.7, 6.4 Hz, 11H). 13C NMR (101 MHz, CDC13) δ 174.18, 173.51, 77.54, 77.23, 76.91, 74.50, 63.12, 59.10, 45.55, 34.81, 34.66, 34.38, 33.76, 32.67, 32.62, 32.45, 29.77, 29.73, 29.64, 29.49, 29.39, 26.42, 25.57, 25.24, 23.23, 22.89, 14.32. Molecular weight for C47H88N06 (M+H)+ Calc. 762.6612, Found 762.5.
Example 31: Synthesis of alcohol components
Figure imgf000192_0001
Compound 2: Compound 2 was synthesized from 1 using a procedure analogous to that described in Journal of the Organic Chemistry, 2009, 1473.
1H NMR (400 MHz, CDC13) δ 3.66 (s, 3 H), 2.23 (d, J = 6.9 Hz, 2 H), 1.84 (brs, 1 H), 1.27 (d, J = 11.5 Hz, 16 H), 0.88 (t, J = 6.8 Hz, 6 H). 13C NMR (100 MHz, CDC13) δ 174.29, 51.49, 39.25, 35.22, 34.00, 32.24, 26.34, 22.77, 14.22.
Compound 3: To a suspension of LiAlH4 (2.84 g, 74.9 mmol) in THF (85 mL) was added a solution of compound 2 (8.55 g, 37.4 mmol) in THF (25 mL). The reaction mixture was refluxed overnight. Aqueous workup then column chromatography gave pure compound 3 (7.35 g, 36.7 mmol, 98%) as a colorless oil.
1H NMR (400 MHz, CDC13) δ 3.66 (t, J = 7.0 Hz, 2 H), 1.59 - 1.12 (m, 19 H), 0.88 (t, J = 6.9 Hz, 6 H).
Compound 4: Tetrahydrolavandulol (10.1 g, 63.8 mmol) was treated with methansulfonyl chloride (6.38 mL) in CH2CI2 (200 mL) and Et N (17.6 mL). Aqueous workup gave the crude mesylate, which was treated with KCN (4.98 g, 76.5 mmol) in EtOH (90 mL) and H20 (10 mL). Aqueous workup then column chromatography gave pure compound 4 (8.36 g, 50.0 mmol, 72%) as a colorless oil.
1H NMR (400 MHz, CDC13) δ 2.38 - 2.23 (m, 2 H), 1.86 - 1.78 (m, 1 H), 1.59 - 1.42 (m, 3 H), 1.40 - 1.07 (m, 3 H), 0.93 - 0.89 (m, 12 H). 13C NMR (100 MHz, CDC13) δ 119.73, 41.69, 36.46, 30.10, 28.44, 28.33, 22.82, 22.59, 19.62, 19.11, 19.05.
Compound 6: The cyano derivative 4 was converted to the ethyl ester under acidic conditions to give compound 5 and the ester was reduced by LiAlH4 in THF to give compound 6.
Compound 7: Tetrahydrolavandulol (98.1 g, 51.2 mmol) was oxidized with PCC (16.6 g, 76.8 mmol) in CH2C12 (200 mL). Aqueous workup then column chromatography gave pure compound 7 (6.19 g, 39.6 mmol, 77%) as a colorless oil.
1H NMR (400 MHz, CDC13) δ 9.60 (d, J = 3.1 Hz, 1 H), 2.05 - 1.79 (m, 1 H), 1.71 - 1.36 (m, 4 H), 1.23 - 1.04 (m, 2 H), 1.02 - 0.82 (m, 12 H).
Compound 9: To a solution of compound 7 (2.0 g, 12.8 mmol) in toluene (40 mL) and CH2C12 (18 mL) and was added 8 (3.96 g, 11.8 mmol). The mixture was heated at 70 °C overnight. Column chromatography gave pure compound 9 (1.40 g, 6.59 mmol, 51%) as a colorless oil.
1H NMR (400 MHz, CDC13) δ 6.77 (dd, J = 15.6, 9.9 Hz, 1 H), 5.76 (d, J = 15.6 Hz, 1 H), 3.73 (s, 3 H), 1.97 - 1.83 (m, 1 H), 1.72 - 1.64 (m, 1 H), 1.54 - 1.40 (m, 2 H), 1.37 - 1.22 (m, 1 H), 1.18 - 0.97 (m, 2 H), 0.94 - 0.78 (m, 12 H). 13C NMR (100 MHz, CDC13) δ 167.19, 152.54, 121.70, 51.53, 49.66, 36.95, 31.76, 29.49, 28.29, 22.92, 22.54, 20.84, 19.24.
Compound 10: To a solution of compound 9 (1.0 g, 4.71 mmol) in MeOH (15 mL) was added Pd-C (125 mg). The mixture was stirred under H2 atmosphere overnight. The mixture was filtered over Celite then evaporated to give pure compound 10 (924 mg, 4.31 mmol, 92%) as a colorless oil. 1H NMR (400 MHz, CDC13) δ 3.67 (s, 3 H), 2.41 - 2.16 (m, 2 H), 1.74 - 1.57 (m, 2 H), 1.57 - 1.42 (m, 2 H), 1.33 - 1.02 (m, 5 H), 0.88 - 0.83 (m, 12 H). 13C NMR (100 MHz, CDC13) δ 174.78, 51.62, 43.71, 36.97, 32.69, 29.23, 28.56, 27.94, 25.92, 22.85, 22.79, 19.32, 19.19.
Compound 11: To a suspension of L1AIH4 (444 mg, 11.7 mmol) in THF (12 mL) was added a solution of compound 10 (1.25 g, 5.83 mmol) in THF (8 mL). The reaction mixture was refluxed overnight. Aqueous workup gave the crude compound 11 (1.1 g) as a colorless oil.
1H NMR (400 MHz, CDC13) δ 3.63 (t, J = 6.7 Hz, 2 H), 1.74 - 1.66 (m, 1 H), 1.60 - 1.45 (m, 3 H), 1.37 - 1.05 (m, 7 H), 0.88 - 0.82 (m, 12 H). 13C NMR (100 MHz, CDC13) δ 63.75, 44.00, 37.16, 31.22, 29.40, 28.61, 28.28, 26.62, 22.90, 22.82, 19.43, 19.28.
Example 32: Synthesis of ester-containing lipids
Figure imgf000194_0001
I TFA cH2ci2
Figure imgf000194_0002
Compound 26: Compound 25 (840 mg, 1.03 mmol) was stirred in TFA (9 mL) and
CH2CI2 (36 mL) for 3 h at room temperature. Evaporation of the solvents and co-evaporation with toluene 3 times gave compound 26.
Molecular weight for C43H8oN06 (M+H)+ Calc. 706.5986, Found 706.4. Compound 27: Compound 26 from the previous step was treated with 2,2- dimethylpropanol (363 mg, 4.12 mmol) in the presence of EDCI (592 mg, 3.09 mmol), DMAP (50 mg, 0.412 mmol) and DIEA (1.44 mL, 8.24 mmol) in CH2C12 (10 mL) for 14 h. Aqueous work-up then column chromatography gave compound 27 (575 mg, 0.679 mmol, 66%).
1H NMR (400 MHz, CDC13) δ 5.40 - 5.28 (m, 4 H), 4.91 - 4.81 (m, 1 H), 3.76 (s, 4 H), 2.34 - 2.27 (m, 8 H), 2.22 (s, 6 H), 2.03 - 1.97 (m, 8 H), 1.83 - 1.26 (m, 50 H), 0.94 (s, 18 H). 13C NMR (100 MHz, CDC13) δ 174.14, 173.53, 130.09, 129.92, 74.41, 73.72, 59.12, 45.61, 34.60, 34.32, 32.64, 31.45, 29.93, 29.85, 29.71, 29.68, 29.48, 29.32, 29.28, 27.39, 27.33, 26.62, 25.52, 25.22, 23.32.
Molecular weight for C53H10oN06 (M+H)+ Calc. 846.7551, Found 846.5.
Example 33: Synthesis of quaternary lipids
A. The amino lipids synthesized in Examples 31 and 32 can be converted to the corresponding quaternary lipids as shown below by treatment with CH3C1 in CH3CN and CHC13.
Figure imgf000196_0001
5: n = 3, p=3, R = H 15Q: n = 3, p=3, R = H
: n = 3, p= 1,R: Me 24Q: n = 3, p= 1, R= Me
Figure imgf000196_0002
: m 16Q: m : m 19Q: m : m 20Q: m : m 21Q: m : m 22Q: m
Figure imgf000196_0003
17: n 17Q: n = 1 18: n 18Q: n = 3
iPr, t-Bu, other alkyl/allyl groups
Figure imgf000196_0004
27TQ
Synthesis of BODIPY-lipid conjugates
Figure imgf000197_0001
Compound 102: To a solution of compound 101 (2.00 g, 4.30 mmol) and ci5,-2-nonen- l- ol (1.81 mL, 10.7 mmol) in CH2CI2 (20 mL) were added diisopropylethylamine (3.00 mL, 17.2 mmol), N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (2.06 g, 10.7 mmol) and DMAP (106 mg, 0.868 mmol). The reaction mixture was stirred at room temperature for 18 hours. The reaction mixture was diluted with CH2CI2 (200 mL) and washed with saturated NaHCC"3 aq. (100 mL). The organic layer was dried over MgS04, filtered and concentrated. The crude was purified by silica gel column chromatography (0-5% EtOAc in Hexane) to give compound 102 (2.11 g, 2.96 mmol, 69%, Rf = 0.45 developed with 10% EtOAc in Hexane).
1H NMR (500 MHz, CDC13) δ 5.67 - 5.61 (m, 2 H), 5.54 - 5.49 (m, 2 H), 4.89 - 4.84 (m, 1 H), 4.62 (d, J = 6.5 Hz, 4 H), 3.46 (t, J = 6.5 Hz, 2 H), 2.48 (t, J = 7.3 Hz, 2 H), 2.30 (t, J = 7.5 Hz, 4 H), 2.20 - 2.14 (m, 2 H), 2.12 - 2.04 (m, 4 H), 1.63 - 1.60 (m, 4 H), 1.51 - 1.50 (m, 4 H), 1.37 - 1.27 (m, 32 H), 0.88 (t, J = 6.8 Hz, 6 H). 13C NMR (100 MHz, CDC13) δ 173.90, 172.45, 135.58, 123.51, 74.74, 60.36, 34.47, 34.24, 32.93, 32.91, 31.83, 29.54, 29.48, 29.31, 29.21, 29.01, 28.03, 27.70, 25.43, 25.08, 22.76, 14.23.
Molecular weight for CsgHegBrNaOe (M+Na)+ Calc. 735.42, Found 735.2. Compound 103: To a solution of 102 (2.11 g, 2.96 mmol) in DMF (20 mL) was added a solution of N-Boc-l,6-diaminohexane (670 mg, 3.10 mmol) in DMF (20 mL) at 0 °C. The mixture was stirred for 18 hours at room temperature. Then additional N-Boc-l,6-diaminohexane (160 mg, 0.740 mmol) in DMF (1 mL) was added and the mixture was stirred for 12 hour. The reaction was quenched by adding saturated NaHC03 aq. (100 mL) then extracted with Et20 (150 mL x 3). The organic layer was separated and dried over anhydrous MgS04. After filtration and concentration, the crude was purified by silica gel column chromatography (5% MeOH in CH2C12, Rf = 0.24) to give 103 (1.28 g, 1.51 mmol, 51%).
1H NMR (400 MHz, CDC13) δ 5.67 - 5.61 (m, 2 H), 5.55 - 5.50 (m, 2 H), 4.88 - 4.81 (m, 1 H), 4.61 (d, J = 6.8 Hz, 4 H), 4.54 (brs, 1 H), 3.11 - 3.08 (m, 2 H), 2.67 - 2.59 (m, 4 H), 2.35 (t, J = 7.4 Hz, 2 H), 2.29 (t, J = 7.6 Hz, 4 H), 2.10 - 2.07 (m, 4 H), 1.84 - 1.81 (m, 4 H), 1.63 - 1.57 (m, 4 H) 1.50 - 1.47 (m, 8 H), 1.44 (s, 9 H), 1.38 - 1.27 (m, 34 H), 0.88 (t, J = 6.8 Hz, 6 H). 13C NMR (100 MHz, CDC13) δ 173.90, 173.53, 135.57, 123.50, 74.49, 60.36, 49.82, 49.29, 40.64, 34.47, 34.24, 32.68, 31.83, 30.16, 29.89, 29.54, 29.50, 29.33, 29.23, 29.01, 28.58, 27.69, 27.11, 26.80, 25.44, 25.37, 25.09, 22.76, 14.23.
Molecular weight for C5oH93N208 (M+H)+ Calc. 849.69, Found 849.5.
Compound 104: To a solution of 103 (1.16 g, 1.37 mmol) in THF (20 mL) were added formaldehye (37 wt. % in H20, 0.306 mL, 4.11 mmol), sodium cyanoborohydride (1 M solution in THF, 2.06 mL, 2.06 mmol) and acetic acid (0.008 mL, 0.137 mmol) at 0 °C. The mixture was stirred at room temperature for 17 hours. The reaction was quenched by adding saturated NaHC03 aq. (50 mL) then extracted with Et20 (100 mL x 3). The organic layer was separated and dried over anhydrous MgS04. After filtration and concentration, the crude was purified by silica gel column chromatography (8% MeOH in CH2C12, Rf = 0.46) to give 104 (531 mg, 0.615 mmol, 45%).
1H NMR (400 MHz, CDC13) δ 5.66 - 5.60 (m, 2 H), 5.53 - 5.47 (m, 2 H), 4.86 - 4.80 (m, 1 H), 4.61 - 4.59 (m, 5 H), 3.12 - 3.07 (m, 2 H), 2.89 - 2.78 (m, 4 H), 2.62 (s, 3 H), 2.40 (t, J = 6.8 Hz, 2 H), 2.28 (t, J = 7.4 Hz, 4 H), 2.11 - 2.06 (m, 4 H), 1.99 - 1.92 (m, 2 H), 1.69 - 1.27 (m, 57 H), 0.87 (t, J = 6.8 Hz, 6 H). 13C NMR (100 MHz, CDC13) δ 173.86, 172.45, 156.18, 135.55, 123.45, 75.24, 60.32, 56.68, 55.83, 40.72, 40.36, 34.40, 34.09, 31.79, 31.29, 29.92, 29.49, 29.41, 29.26, 29.17, 28.96, 28.55, 27.65, 26.49, 26.30, 25.41, 25.02, 24.79, 22.71, 20.12, 14.19.
Molecular weight for C51H95N2O8 (M+H)+ Calc. 863.71, Found 863.6.
Compound 105: To a solution of compound 104 (525 mg, 0.608 mmol) in CH2C12 (8 mL) was added trifluoro acetic acid (2 mL) at 0 °C. The reaction mixture was stirred at 0 °C for 1 hour and at room temperature for 3 hours. The reaction mixture was evaporated and co- evaporated with toluene 3 times then dried in vacuo overnight to give compound 105 (603 mg, 0.603 mmol calculated as 2 TFA salt, quantitatively, Rf = 0.24 developed with 8% MeOH in CH2C12).
1H NMR (400 MHz, CDC13) δ 8.06 (brs, 1 H), 5.68 - 5.61 (m, 2 H), 5.55 - 5.49 (m, 2 H), 4.87 - 4.81 (m, 1 H), 4.62 (d, J = 6.8 Hz, 4 H), 4.28 (brs, 3 H), 3.20 - 3.02 (m, 6 H), 2.82 (d, J = 4.0 Hz, 3 H), 2.45 - 2.40 (m, 2 H), 2.30 (t, J = 7.4 Hz, 4 H), 2.12 - 2.00 (m, 6 H), 1.78 - 1.22 (m, 52 H), 0.88 (t, J = 6.8 Hz, 6 H). 13C NMR (100 MHz, CDC13) δ 174.04, 172.08, 161.84, 161.47, 135.63, 123.44, 117.60, 114.71, 75.56, 60.41, 55.69, 55.27, 39.94, 39.64, 34.44, 34.06, 31.82, 30.72, 29.53, 29.43, 29.28, 29.19, 29.00, 27.69, 26.58, 25.42, 25.27, 25.05, 24.60, 23.06, 22.75, 19.00, 14.22.
Molecular weight for C46H87N206 (M+H)+ Calc. 763.66, Found 763.4.
Compound 106: To a solution of 105 (23.8 mg, 0.0240 mmol, calculated as 2TFA salt) in CH2C12 (1 mL) and Et3N (0.050 mL, 0.360 mmol) was added a solution of BODIPY® 493/503 (10 mg, 0.0240 mmol, Life Technology #D2191) in CH2C12 (2 mL). The reaction mixture was stirred for 1 h. The reaction mixture was loaded onto silica gel column chromatography and eluted with 0-5% MeOH in CH2C12. The product color fractions were collected (5% MeOH in CH2C12, Rf = 0.36) to give 106 (26 mg, 0.024 mmol, quantitatively).
1H NMR (400 MHz, CDC13) δ 6.05 (s, 2 H), 5.67 - 5.61 (m, 2 H), 5.54 - 5.48 (m, 2 H), 4.85 - 4.82 (m, 1 H), 4.61 (d, J = 6.8 Hz, 4 H), 3.37 - 3.32 (m, 2 H), 3.27 - 3.22 (m, 2 H), 2.51 - 2.44 (m, 17 H)„ 2.34 - 2.27 (m, 8 H), 2.12 - 2.06 (m, 4 H), 1.60 - 1.21 (m, 52 H), 0.88 (t, J = 6.8 Hz, 6 H).
Molecular weight for C62H104BF2N4O7 (M+H)+ Calc. 1065.80, Found 1065.5. Example 34: Multi-ester containin Lipids and Acetal linked lipids
Figure imgf000200_0001
Figure imgf000200_0002
Synthesis of compound 5002: To a stirred solution of alcohol 5001 (1.0 g, 5.15 mmol), Glycolic anhydride 5000 (5.66 mmol) in DCM (20 mL) was added DMAP (1.26 g, 10.41 mmol) and stirred at room temperature for 48 h. The reaction mixture was concentrated followed by column purification gave the corresponding product 5002 (1.4 g, 86 %) as DMAP salt. LCMS: Calculated: 316.22 (M+), Found: 315.1 (M+-l).
Synthesis of compound 5004: To a stirred solution of alcohol 5003 (5.0 g, 44.6 mmol), 4- (Dimethylamino)butyric acid hydrochloride (8.1 g, 48.3 mmol) and EDC (10.3 g, 53.6 mmol) in DCM (100 mL) was added DIEPA (23 g, 178.3 mmol) and stirred at room temperature overnight. After usual work up, the crude product was purified by column chromatography (9.0 g, 90 %).
Synthesis of compound 5005: To a stirred solution of diene 5004 (4.0 g, 18 mmol) in 10 mL of THF was added 9-BBN and stirred overnight. To the above solution was added 6.6 mL of 3M NaOAc and 7.4 mL of 30 % Η202 at 0-5° C. The reaction mixture was stirred at room temperature overnight. After usual work up, the crude material was purified by column chromatography to get 5005 (2.6 g, 55 %) as viscous oil. LCMS: Calculated: 261.19 (M+), Found: 262.1 (M++l). Synthesis of compound 5006 and 5007: To a stirred solution of diene 5005 (260 mg, 1 mmol), acid 5002 (1.0 g, 2.28 mmol), EDC (387 mg, 2 mmol) in 10 mL of DCM was added DIEA (516 mg, 4 mmol) and stirred overnight. After usual work up, the crude material was purified by column chromatography to get 5006 (0.1 g, 12 %) and 5007 (0.2 g, 36 %). LCMS for compound 5006: Calculated: 857.62 (M+), Found: 858.5 (M++l), 880.5 (M++Na). LCMS for compound
+), Found: 560.4 (M++l).
Figure imgf000201_0001
Synthesis of compound 5011: To a stirred solution of alcohol 5008 (2.66 g 10 mmol) in 5 mL of Chlorotrimethylsilane was added paraformaldehyde (0.3 g, 10 mmol) and stirred at room temperature overnight. The excess Chlorotrimethylsilane was evaporated followed by drying under reduced pressure gave the corresponding product 5009 and used for next step without purification. The compound 5009 was added dropwise to the solution of diol (261 mg, 1 mmol), DIEA (2.5 g, 19.4 mmol) and DMAP (20 mg, 0.16 mmol) in DCM (10 mL) and stirred overnight. Concentration of the solvent gave the crude product 5010, which was dissolved in 5 mL of THF and 2 mL of IN NaOH was added and stirred for 2 days at room temperature. After usual work up, the crude material was purified by column chromatography to get the corresponding product 5011 (200 mg, 28 %). LCMS for compound 5010: Calculated: 1131.95 (M+), Found: 1096.98 (M+ -CI")). LCMS for compound 5011: Calculated: 704.63 (M+), Found: 727.5 (M++Na).
Synthesis of compound 5012: To a stirred solution of alcohol 5011 (200 mg, 0.284 mmol), 4- (Dimethylamino)butyric acid hydrochloride (103 mg, 0.57 mmol), EDC (109 mg, 0.57 mmol) in 10 mL of DCM was added DIEA (294 mg, 4 mmol) and stirred overnight. After usual work up, the crude material was purified by column chromatography to get 5012 (190 mg, 85 %). LCMS for compound 5012: Calculated: 817.72 (M+), Found: 818.5 (M++Na).
Figure imgf000202_0001
5018
Synthesis of compound 5016: To a stirred solution of alcohol 5013 (1.0 g 7.03 mmol) in 5 mL of Chlorotrimethylsilane was added acetaldehyde (0.3 g, 7.03 mmol) and stirred at room temperature for 2 h. The excess Chlorotrimethylsilane was evaporated followed by drying under reduced pressure gave the corresponding product 5014 and used for next step without purification. The compound 5014 was added dropwise to the solution of diol 5015(223 mg, 0.55 mmol), DIEA (2 mL g, 11.5 mmol) and DMAP (20 mg, 0.16 mmol) in DCM (10 mL) and stirred overnight. 10 mL of water was added followed by extraction with DCM (3 X 30 mL), washed with water, saturated NaHC03, brine and dried over anhydrous Na2S04. Concentration of the solvent gave the crude product, which was used for the next step without purification. LCMS for compound 5016: Calculated: 738.66 (M+), Found: 761.5 (M++Na).
Synthesis of compound 5017: To a stirred solution of alcohol 5016 in 5 mL of THF was added
0.54 mL of 1M TBAF in THF (0.54 mmol) and stirred for 2 days at room temperature. After usual work up, the crude material was purified by column chromatography to get 5017.
However, it contains some inseparable impurity and hence used for next step without further purification. LCMS for compound 5017: Calculated: 624.57 (M+), Found: 647.5 (M++Na).
Synthesis of compound 5018: To a stirred solution of alcohol 5017 (0.55 mmol), 4-
(Dimethylamino)butyric acid hydrochloride (116 mg, 0.64 mmol), EDC (123 mg, 0.64 mmol) in
10 mL of DCM was added DIEA (165 mg, 1.28 mmol) and stirred for 2 days. After usual work up, the crude material is purified by column chromatography (0-10 % MeOH in 1 % Et3N containing DCM) to get 5018 (300 mg, 75 % from 5015). LCMS for compound 5018:
Calculated: 737.65 (M+), Found: 738.6 (M++l), 760.5 (M++Na+). Example 35: Preparation of Lipid Nanoparticles
The cationic lipids described herein are used to formulate liposomes containing the AD- 1661 duplex (shown in the table below) using an in-line mixing method as described in International Publication No. WO 2010/088537, which is incorporated by reference in its entirety. The lipid nanoparticles had the formulation shown in the table below.
Figure imgf000203_0001
The siRNA AD-1661 duplex has the sequence shown below.
Figure imgf000203_0002
Lower case is 2'OMe modification and Nf is a 2'F modified nucleobase, dT is deoxythymidine, s is phosphothioate
The lipid nanoparticles was prepared as follows. Cationic lipid, DSPC, cholesterol, and PEG-DMG in the ratio recited in the table above were solubilized in ethanol at a total lipid concentration of 25 mg/niL.
A siRNA stock solution was prepared by solubilizing the siRNA AD-1661 in a low pH acetate or citrate buffer (pH=4) at 0.8 mg/niL. The stock solutions should be completely clear and the lipids should be completely solubilized before combining with the siRNA. Therefore, if it was determined appropriate, the stock solutions were heated to completely solubilize the lipids.
The individual stock solutions were combined by pumping each solution to a T-junction (i.e., by in-line mixing). Specifically, the ethanol solution (at 5 ml/min, via 0.01 in. PEEK tube) and aqueous buffer solution (at 15 mL/min, via 0.02 in. PEEK tube) were mixed through a T- junction (PEEK Tee body, IDEX).
After the T-junction a single tubing is placed where the combined stream will emit. Ethanol is removed and exchanged for PBS by dialysis. The lipid formulations are then concentrated using centrifugation or diafiltration to an appropriate working concentration.
Lipid nanoparticles containing the cationic lipids listed in the table in Example 36 were prepared as described above.
Example 36: Efficacy of Lipid Nanoparticles
Factor VII (FVII), a prominent protein in the coagulation cascade, is synthesized in the liver (hepatocytes) and secreted into the plasma. FVII levels in plasma can be determined by a simple, plate-based colorimetric assay. As such, FVII represents a convenient model for determining siRNA-mediated downregulation of hepatocyte-derived proteins.
Test formulations of the lipid nanoparticles prepared in Example 35 were initially assessed for their FVII knockdown in female 7-9 week old, 15-25g, female C57B1/6 mice at 0.1, 0.3, 1.0 and 5.0 mg/kg with 3 mice per treatment group. All studies included animals receiving either phosphate-buffered saline (PBS, control group) or a benchmark formulation. Formulations were diluted to the appropriate concentration in PBS immediately prior to testing. Mice were weighed and the appropriate dosing volumes calculated (10 μΐ/g body weight). Test and benchmark formulations as well as PBS (for control animals) were administered intravenously via the lateral tail vein. Animals were anesthetised 24 hours later with an intraperitoneal injection of ketamine/xylazine and 500-700 μΐ of blood was collected by cardiac puncture into serum separator tubes (BD Microtainer). Blood was centrifuged at 2,000 x g for 10 minutes at 15° C and serum was collected and stored at -70° C until analysis. Serum samples were thawed at 37° C for 30 minutes, diluted in PBS and aliquoted into 96-well assay plates. Factor VII levels were assessed using a chromogenic assay (Biophen FVII kit, Hyphen BioMed) according to the manufacturer's instructions and absorbance was measured in a microplate reader equipped with a 405 nm wavelength filter. Plasma FVII levels were quantified and ED50 values (dose resulting in a 50% reduction in plasma FVII levels compared to control animals) were calculated using a standard curve generated from a pooled sample of serum from control animals. Those formulations of interest showing high levels of FVII knockdown (ED50 « 0.1 mg/kg) were re-tested in independent studies at a lower dose range to confirm potency and establish ED50 levels.
The following table shows ED50 values for some of the cationic lipids described herein. Two asterisks (**) indicates an ED50 value between 0.001 and 0.10. One asterisk (*) indicates an ED50 value greater than 0.10.
Figure imgf000205_0001
Figure imgf000206_0001
Figure imgf000207_0001
Figure imgf000208_0001
Example 37: Hydrophobicity and Stability The logP values for the biodegrabable cationic lipids listed in the table below were calculated using the software available at http://www.molinspiration.com/services/logp.html from Molinspiration Cheminformatics of Slovensky Grob, Slovak Republic.
Furthermore, the HPLC retention time for each biodegradable cationic lipid was measured in lipid nanoparticles prepared from them. The lipid nanoparticles were prepared as described in Example 35 using AD- 1661 as the payload. The retention times are reported in the table below relative to the retention time for cholesterol.
The HPLC buffer used was a mixture of two solutions (Solution #1 and Solution #2).
Solution #1: 80% methanol / 20% 10 mM NH4HC03
Solution #2: 80% methanol / 20% isopropanol The ratios of the two solutions in the mixture changed over time as indicated in the table below.
Time (min) Solution #1 (vol%) Solution #2 (vol%) 0 70 30 4 10 90 6 10 90
6.1 70 30
8 70 30
The size of the lipid nanoparticles was measured before and after undergoing dialysis overnight. In general, greater changes in lipid nanoparticle size are indicative of lesser stability.
Dynamic laser light scattering was used to determine the lipid nanoparticle size (expressed as the intensity weighted diameter) with a Zetasizer (Malvern Instruments, Inc. of Westborough, MA). All measurements were made at 532 nm wavelength at the scattering angle of 173° using normal resolution mode as the analysis model. The results of these experiments are provided in the table below.
Figure imgf000210_0001
Figure imgf000211_0001
These and other changes can be made to the embodiments in light of the above-detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.

Claims

WHAT IS CLAIMED IS:
1. A compound of the formula:
Figure imgf000212_0001
Formula (III) or a salt thereof, wherein
R' is absent, hydrogen, or CrC4 alkyl; with respect to R 1 and R 2 ,
(i) R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R10;
(ii) R 1 and R 2 , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring; or
(iii) one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl with (a) the adjacent nitrogen atom and (b) the (R)a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR3R4)-; each occurrence of R3 and R4 are, independently H, halogen, OH, alkyl, alkoxy, -NH2, R10, alkylamino, or dialkylamino; each occurrence of R is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein (i) the PEG or polymer is linear or branched, (ii) the PEG or polymer is polymerized by n subunits, (iii) n is a number- averaged degree of polymerization between 10 and 200 units, and (iv) wherein the compound of formula has at most two R10 groups; the dashed line to Q is absent or a bond; when the dashed line to Q is absent then Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0-
, -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, - OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-; or when the dashed line to Q is a bond then (i) b is 0 and (ii) Q and the tertiary carbon adjacent to it (C*) form a substituted or unsubstituted, mono- or bi-cyclic heterocyclic group having from 5 to 10 ring atoms; each occurrence of R5 is, independently, H or Ci-C4 alkyl;
1 2
M and are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - 1
OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000213_0001
(wherein R is a C2- Cg alkyl or alkenyl)); each occurrence of Rz is, independently, C Cg alkyl; a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3;
1 2
L and I are each, independently, Q-Cs alkylene or C2-C5 alkenylene; X and Y are each, independently, C4-C20 alkylene or C4-C20 alkenylene; and
Z 1 and Z 2 are each, independently, C8-C14 alkyl or C8-C14 alkenyl, wherein the alkenyl group may optionally be substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of Z 1 or Z 2 , and with the proviso that the terminus of at least one of Z 1 and Z2 is separated from the group M 1 or M2 by at least 8 carbon atoms.
2. The compound of claim 1, wherein L 1 and L 2 are each -CH2-.
3. The compound of claim 1, wherein L 1 and L 2 are each -(CH2)2- or -(CH2)3-.
4. The compound of any of claims 1-3, wherein X and Y are each, independently - (CH2)n wherein n is 4, 5, 6, 7 or 8.
5. The compound of claim 4, wherein X and Y are -(CH2)7-, -(CH2)8-, or -(CH2)cr.
6. A com ound of the formula:
Figure imgf000214_0001
Formula (IIIA) or a salt thereof, wherein
R' is absent, hydrogen, or C C4 alkyl; with respect to R 1 and R 2 ,
(i) R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R10; 1 2
(ii) R and R , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring; or
1 2
(iii) one of R and R is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4- 10 member heterocyclic ring or heteroaryl with (a) the adjacent nitrogen atom and (b) the (R)a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR3R4)-; each occurrence of R3 and R4 are, independently H, halogen, OH, alkyl, alkoxy, -NH2, R10, alkylamino, or dialkylamino; each occurrence of R10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein (i) the PEG or polymer is linear or branched, (ii) the PEG or polymer is polymerized by n subunits, (iii) n is a number- averaged degree of polymerization between 10 and 200 units, and (iv) wherein the compound of formula has at most two R10 groups; the dashed line to Q is absent or a bond; when the dashed line to Q is absent then Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0- , -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, - OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-; or when the dashed line to Q is a bond then (i) b is 0 and (ii) Q and the tertiary carbon adjacent to it (C*) form a substituted or unsubstituted, mono- or bi-cyclic heterocyclic group having from 5 to 10 ring atoms; each occurrence of R5 is, independently, H or Q-C4 alkyl;
1 2
M and are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, -
SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-,
-C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000216_0001
(wherein R11 is a C2-
C8 alkyl or alkenyl));
each occurrence of Rz is, independently, C Cg alkyl;
a is 1, 2, 3, 4, 5 or 6;
b is 0, 1, 2, or 3;
each Rz is, independently, Ci-Cg alkyl;
1 and V 2
L are each, independently, Q-Cs alkylene or C2-C5 alkenylene;
X and Y are each, independently, C4-C20 alkylene or C4-C2o alkenylene; and
1 2
Z and Z are each, independently, Ci-C% alkyl or C2-C8 alkenyl;
wherein said cationic lipid is not one selected from:
Figure imgf000216_0002
Figure imgf000217_0001
7. The compound of claim 6, wherein L 1 and L 2 are each -(CH2)2-.
8. The compound of claim 6, wherein L 1 and L 2 are each -(CH2)3-.
9. The compound of any one of claims 6-8, wherein X and Y are each, independently, -(CH2)n- wherein n is 7-9.
10. The compound of any one of claims 6-9, wherein M1 and M2 are -C(0)0- (where
1 1 2 the carbonyl group in M and M" is bound to the variable X, and the oxygen atom in M and M is bound to the variable L 1 and L 2 ). 1 2
11. The compound of any one of claims 6-10, wherein the R'R R N-(R)a-Q-(R)t>- group is selected from (CH3)2N-(CH2)3-C(0)0-, (CH3)2N-(CH2)2-NH-C(0)0-, (CH3)2N-(CH2)2- OC(0)-NH-, and (CH3)2N-(CH2)3-C(CH3)=N-0-.
12. The compound of any one of claims 6-11, wherein Z1, Z2, and each Rz are C3-C8 alkyl.
13. The compound of claim 12, wherein Z1, Z2, and each Rz are C3-C6 alkyl.
14. A compound of the formula:
Figure imgf000218_0001
Formula (IV) or a salt thereof, wherein
R' is absent, hydrogen, or CrC4 alkyl; with respect to R 1 and R 2 ,
(i) R 1 and R 2 are each, independently, optionally substituted alkyl, alkenyl, alkynyl, cycloalkylalkyl, heterocycle, or R10;
(ii) R 1 and R 2 , together with the nitrogen atom to which they are attached, form an optionally substituted heterocylic ring; or
(iii) one of R 1 and R 2 is optionally substituted alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkylalkyl, or heterocycle, and the other forms a 4-10 member heterocyclic ring or heteroaryl with (a) the adjacent nitrogen atom and (b) the (R)a group adjacent to the nitrogen atom; each occurrence of R is, independently, -(CR3R4)-; each occurrence of R3 and R4 are, independently H, halogen, OH, alkyl, alkoxy, -NH2, R10, alkylamino, or dialkylamino; each occurrence of R10 is independently selected from PEG and polymers based on poly(oxazoline), poly(ethylene oxide), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), poly[N-(2-hydroxypropyl)methacrylamide] and poly(amino acid)s, wherein (i) the PEG or polymer is linear or branched, (ii) the PEG or polymer is polymerized by n subunits, (iii) n is a number- averaged degree of polymerization between 10 and 200 units, and (iv) wherein the compound of formula has at most two R10 groups; the dashed line to Q is absent or a bond; when the dashed line to Q is absent then Q is absent or is -0-, -NH-, -S-, -C(O)-, -C(0)0- , -OC(O)-, -C(0)N(R4)-, -N(R5)C(0)-, -S-S-, -OC(0)0-, -0-N=C(R5)-, -C(R5)=N-0-, - OC(0)N(R5)-, -N(R5)C(0)N(R5)-, -N(R5)C(0)0-, -C(0)S-, -C(S)0- or -C(R5)=N-0-C(0)-; or when the dashed line to Q is a bond then (i) b is 0 and (ii) Q and the tertiary carbon adjacent to it (C*) form a substituted or unsubstituted, mono- or bi-cyclic heterocyclic group having from 5 to 10 ring atoms; each occurrence of R5 is, independently, H or Ci-C4 alkyl;
1 2
M and are each, independently, a biodegradable group (e.g., -OC(O)-, -C(0)0-, - SC(O)-, -C(0)S-, -OC(S)-, -C(S)0-, -S-S-, -C(R5)=N-, -N=C(R5)-, -C(R5)=N-0-, -0-N=C(R5)-, -C(0)(NR5)-, -N(R5)C(0)-, -C(S)(NR5)-, -N(R5)C(0)-, -N(R5)C(0)N(R5)-, -OC(0)0-, - 1
OSi(R5)20-, -C(0)(CR3R4)C(0)0-, -OC(0)(CR3R4)C(0)-, or
Figure imgf000219_0001
C8 alkyl or alkenyl)); each occurrence of Rz is, independently, C Cg alkyl; a is 1, 2, 3, 4, 5 or 6; b is 0, 1, 2, or 3;
1 2
L and L and are each, independently, Q-Cs alkylene or C2-C5 alkenylene;
X and Y are each, independently, alkylene or alkenylene; and each occurrence of Z is independently CrC4 alkyl (preferably, methyl).
15. The compound of claim 14, wherein X and Y are C12-C2o alkylene or C12-C2o alkenylene.
16. The compound of claim 14 or 15, wherein -L1-C(Z)3 is -CH2C(CH3)3 or - CH2CH2C(CH3)3.
17. A cationic lipid or a salt thereof having:
(i) a central carbon atom,
(ii) a nitrogen containing head group directly bound to the central carbon atom, and
(iii) two hydrophobic tails directly bound to the central carbon atom, wherein each hydrophobic tail is of the formula -Re-M-Rf where Re is a C4-C14 alkyl or alkenyl, M is a biodegradable group, and Rf is a branched alkyl or alkenyl, such that (i) the chain length of -Re- M-Rf is at most 20 atoms, and (ii) the group -Re-M-Rf has at least 20 carbon atoms, wherein the alkyl or alkenyl group in Re is optionally substituted with one or two fluorine atoms at
1 2
the alpha position to the M or M group; and the alkenyl group in R is optionally substituted with one or two fluorine atoms at the alpha position to a double bond which is between the double bond and the terminus of R .
18. A compound selected from:
Figure imgf000221_0001
Figure imgf000221_0002
Figure imgf000221_0003
Figure imgf000221_0004
-220- Ίί' o o o
Figure imgf000222_0001
Figure imgf000222_0002
Y 7Γ
0
'If 0
Figure imgf000222_0003
Figure imgf000223_0001
Figure imgf000223_0002
Figure imgf000223_0003
_ 9 0
Figure imgf000224_0001
r = 0-2, n = 1-5, and m = 1-5
Figure imgf000226_0001
Figure imgf000227_0001
-226-
Figure imgf000228_0001
-227 -
Figure imgf000229_0001
-228 -
Figure imgf000230_0001
Figure imgf000231_0001
Figure imgf000232_0001
Figure imgf000233_0001
Figure imgf000234_0001
-233 -
Figure imgf000235_0001
and salts thereof.
20. The compound of any of the preceding claims, wherein the compound is in the form of a pharmaceutically acceptable salt.
21. The compound of any of the preceding claims, wherein the compound is in the form of a cationic lipid.
22. A lipid particle comprising a neutral lipid, a lipid capable of reducing aggregation, and a cationic lipid of claim 21.
23. The lipid particle of claim 22, wherein the neutral lipid is selected from DSPC, DPPC, POPC, DOPE, or SM; the lipid capable of reducing aggregation is a PEG lipid; and the lipid particle further comprises a sterol.
24. The lipid particle of any one of claims 22 and 23, wherein the cationic lipid is present in a mole percentage of about 20% and about 60%; the neutral lipid is present in a mole percentage of about 5% to about 25%; the sterol is present in a mole percentage of about 25% to about 55%; and the PEG lipid is PEG-DMA, PEG-DMG, or a combination thereof, and is present in a mole percentage of about 0.5% to about 15%.
25. The lipid particle of claim 22, wherein the lipid capable of reducing aggregation is PEG-DMG.
26. The lipid particle of claim 25, wherein the lipid particle comprises about 50 mole % of the cationic lipid, about 10% DSPC, about 38.5% cholesterol, and about 1.5% PEG-DMG (based on 100% of the lipid components in the lipid particle).
27. The lipid particle of any of claims 22-26, further comprising an active agent.
28. The lipid particle of claim 27, wherein the active agent is a nucleic acid selected from a plasmid, an immuno stimulatory oligonucleotide, an siRNA, an antisense oligonucleotide, a microRNA, an antagomir, an aptamer, and a ribozyme.
29. A pharmaceutical composition comprising a lipid particle of any one of claims 22-28 and a pharmaceutically acceptable carrier.
30. A method of modulating the expression of a target gene in a cell, comprising providing to the cell a lipid particle of any one of claims 22-28.
31. The method of claim 30, wherein the active agent is a nucleic acid is an siRNA.
32. A method of treating a disease or disorder characterized by the overexpression of a polypeptide in a subject, comprising providing to the subject the pharmaceutical composition of claim 29, wherein the active agent is a nucleic acid selected from the group consisting of an siRNA, a microRNA, and an antisense oligonucleotide, and wherein the siRNA, microRNA, or antisense oligonucleotide includes a polynucleotide that specifically binds to a polynucleotide that encodes the polypeptide, or a complement thereof.
33. A method of treating a disease or disorder characterized by underexpression of a polypeptide in a subject, comprising providing to the subject the pharmaceutical composition of claim 29, wherein the active agent is a plasmid that encodes the polypeptide or a functional variant or fragment thereof.
34. A method of inducing an immune response in a subject, comprising providing to the subject the pharmaceutical composition of claim 29, wherein the active agent is an immuno stimulatory oligonucleotide .
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